Re: [gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)
Thank you! I will try to change something and write to you about the result . -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] IMPLICIT SOLVENT IN AMBER
Dear, all I just begin to work in gromacs. I would like to run on a protein with amber99. Is there someone here that successfully did a protein simulation in GROMACS with implicit solvent and willing to explain the procedure and share the parameters used (especially force field). In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp? How to change this parameters correctly? What changes should be done on the previous steps? I mean, how to start a simulation with implicit solvent model from the very beginning? Sorry for primitive question, but I did not found any useful information about it for the begginers. ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] IMPLICIT SOLVENT IN AMBER
Thanks!
If I understand you correctly, I need to do this (?):
1.
pdb2gmx
2.
Adding ions (if I have no SOL, what is better to choose on this step?)
3.
Minimization with mdp file, that includes these lines:
implicit_solvent = GBSA
gb_algorithm = {Still,HCT,OBC}
sa_algorithm=Ace-approximation
4.
Equilibration (nvt, npt) and MD also with these lines in mdp files.
2011/3/10 Per Larsson
> Hi!
>
> Starting an implicit solvent simulation works just as starting a "normal",
> explicit solvent simulation, except there is no solvent molecules.
> You should use version 4.5.3 for this though (4.0.5 will not work).
>
> Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
> grompp, mdrun etc... as you otherwise would do.
> The choice of the Born radii model is set by gb_algorithm = {Still,HCT,OBC}
> and the non-polar solvation is calculated using
> sa_algorithm=Ace-approximation.
>
> Cheers
> /Per
>
> 10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:
>
> Dear, all
> I just begin to work in gromacs.
> I would like to run on a protein with amber99.
> Is there someone here that successfully did a protein simulation in
> GROMACS with implicit solvent and willing to explain the procedure and
> share the parameters used (especially force field).
>
> In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp?
> How to change this parameters correctly?
> What changes should be done on the previous steps? I mean, how to start a
> simulation with implicit solvent model from the very beginning?
> Sorry for primitive question, but I did not found any useful information
> about it for the begginers.
>
> ; IMPLICIT SOLVENT ALGORITHM
> implicit_solvent = No
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Dielectric coefficient of the implicit solvent
> gb_epsilon_solvent = 80
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
> ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
> sa_surface_tension = 2.092
>
> --
>
> Sincerely,
>
> Yulian Gavrilov
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Sincerely,
Yulian Gavrilov
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] IMPLICIT SOLVENT IN AMBER
Thanks again!
Don't you know how to make a total charge = 0 in this case, if implicit salt
concentration is not implemented currently? Or it is not critically?
2011/3/10 Per Larsson
> Hi!
>
> Yes, except that in point 2, I'm not sure about the effects of explicit
> ions in an implicit solvent.
> Do deal with that properly one should use an implicit salt concentration,
> but that is not implemented currently.
> The choice of water-model with pdb2gmx is not important. You can choose
> 'None' here.
>
> Cheers
> /Per
>
> 10 mar 2011 kl. 10.39 skrev Yulian Gavrilov:
>
> Thanks!
>
> If I understand you correctly, I need to do this (?):
>
>1.
>
>pdb2gmx
>2.
>
>Adding ions (if I have no SOL, what is better to choose on this step?)
>3.
>
>Minimization with mdp file, that includes these lines:
>
>implicit_solvent = GBSA
>
>gb_algorithm = {Still,HCT,OBC}
>
>sa_algorithm=Ace-approximation
>4.
>
>Equilibration (nvt, npt) and MD also with these lines in mdp files.
>
>
>
> 2011/3/10 Per Larsson
>
>> Hi!
>>
>> Starting an implicit solvent simulation works just as starting a "normal",
>> explicit solvent simulation, except there is no solvent molecules.
>> You should use version 4.5.3 for this though (4.0.5 will not work).
>>
>> Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
>> grompp, mdrun etc... as you otherwise would do.
>> The choice of the Born radii model is set by gb_algorithm =
>> {Still,HCT,OBC} and the non-polar solvation is calculated using
>> sa_algorithm=Ace-approximation.
>>
>> Cheers
>> /Per
>>
>> 10 mar 2011 kl. 10.10 skrev Yulian Gavrilov:
>>
>> Dear, all
>> I just begin to work in gromacs.
>> I would like to run on a protein with amber99.
>> Is there someone here that successfully did a protein simulation in
>> GROMACS with implicit solvent and willing to explain the procedure and
>> share the parameters used (especially force field).
>>
>> In mdout.mdp (gromacs 4.0.5) I found this lines. Can I add them to md.mdp?
>> How to change this parameters correctly?
>> What changes should be done on the previous steps? I mean, how to start a
>> simulation with implicit solvent model from the very beginning?
>> Sorry for primitive question, but I did not found any useful information
>> about it for the begginers.
>>
>> ; IMPLICIT SOLVENT ALGORITHM
>> implicit_solvent = No
>>
>> ; GENERALIZED BORN ELECTROSTATICS
>> ; Algorithm for calculating Born radii
>> gb_algorithm = Still
>> ; Frequency of calculating the Born radii inside rlist
>> nstgbradii = 1
>> ; Cutoff for Born radii calculation; the contribution from atoms
>> ; between rlist and rgbradii is updated every nstlist steps
>> rgbradii = 2
>> ; Dielectric coefficient of the implicit solvent
>> gb_epsilon_solvent = 80
>> ; Salt concentration in M for Generalized Born models
>> gb_saltconc = 0
>> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>> gb_obc_alpha = 1
>> gb_obc_beta = 0.8
>> gb_obc_gamma = 4.85
>> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>> ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2.
>> sa_surface_tension = 2.092
>>
>> --
>>
>> Sincerely,
>>
>> Yulian Gavrilov
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
>
> Sincerely,
>
> Yulian Gavrilov
>
>
>
--
Sincerely,
Yulian Gavrilov
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] isopeptide bond
Dear gmx users, I just started with gromacs. Can you help me to find my mistake? I already asked about it, but I did not understand what to do exactly in my case. I try to run to add a new *isopeptide bone* to connect Lys and Gly (to make a tetramer of *ubiquitin*). I use AMBER99 force field, Gromacs 4.0.5. What I did: 1. I changed names of residues according to AMBER rules (LYS to LYN etc.). 2. Added new type of residues to ffamber.rtp (LYN -> LYQ and GLY -> GLQ that are making a new isopeptide bond) and added a new line to specbond.dat (LYN NZ 1 GLY C 1 0.13 LYQ GLQ) to make such a bond. 3. Added new bond type, angle type and dihedral type to ffamber99bon.itp After running of MD (I've got good minimization and equilibration – nvt and npt) I've got such an error: starting mdrun 'Protein in water' 60 steps, 1200.0 ps. step 94100, will finish Sun Mar 13 08:15:56 2011 Step 94124, time 188.248 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000796, max 0.032792 (between atoms 2454 and 2456) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2454 2457 35.6 0.1522 0.1545 0.1522 And after it the same type of errors with another atoms: 2454 2456 36.1 0.1106 0.1113 0.1090 --> *Gly CA and HA1, HA2* 2454 2455 40.5 0.1114 0.1103 0.1090 . 2454 2456 90.0 0.1078 0.1479 0.1090 771 773 48.5 0.1011 0.1012 0.1010 .. 771 773 39.8 0.1012 0.1005 0.1010 --> *Gly NZ and HZ1, HZ2* 771 772 34.9 0.1012 0.1030 0.1010 ... 2454 2457 102.1 0.1490 38312886396780544. 0.1522 2454 2456 83.0 5.9313 39290317874135040. 0.1090 ... First errors are with atoms from the residues with *new isopeptide bond*. I suppose, that this bond is not good. Please can you advice me how yo make this isopeptide bond good? Can I just remove this hydrogens? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] isopeptide bond
Thank you! I use the correct “O” in Gly according to .rtp and I checked it with vmd. There is really a new isopeptide bond. When there is no bond, after minimization and equilibration, Gly and Lys just close to each other but they are not connected (in vmd). In my case they are connected (in vmd, pymol). When I look on step...pdb, one these residues is exploded (it's atoms are far from each other outside of the water box). 2011/3/13 Mark Abraham > On 13/03/2011 8:55 PM, Yulian Gavrilov wrote: > > Dear gmx users, > > I just started with gromacs. > > Can you help me to find my mistake? I already asked about it, but I did not > understand what to do exactly in my case. > > I try to run to add a new *isopeptide bone* to connect Lys and Gly (to > make a tetramer of *ubiquitin*). I use AMBER99 force field, Gromacs 4.0.5. > > What I did: > >1. > >I changed names of residues according to AMBER rules (LYS to LYN etc.). > > 2. > >Added new type of residues to ffamber.rtp (LYN -> LYQ and GLY -> GLQ >that are making a new isopeptide bond) and added a new line to specbond.dat >(LYN NZ 1 GLY C 1 0.13 LYQ GLQ) to make such a bond. > > > IIRC, this creates a bond between the lysine side-chain amine N and glycine > *backbone* carbonyl C. You must use the atom name for the side-chain > carbonyl carbon (see .rtp entry for GLY). If you've done this wrong, then > specbond will probably not have made a bond, because the backbone carbonyl C > was too far away. You should check your pdb2gmx output carefully. > > > >1. > 2. > >Added new bond type, angle type and dihedral type to ffamber99bon.itp > > > After running of MD (I've got good minimization and equilibration – nvt > and npt) I've got such an error: > > > starting mdrun 'Protein in water' > > 60 steps, 1200.0 ps. > > step 94100, will finish Sun Mar 13 08:15:56 2011 > > Step 94124, time 188.248 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 0.000796, max 0.032792 (between atoms 2454 and 2456) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 2454 2457 35.6 0.1522 0.1545 0.1522 > > > And after it the same type of errors with another atoms: > > 2454 2456 36.1 0.1106 0.1113 0.1090 --> *Gly CA and HA1, HA2* > > 2454 2455 40.5 0.1114 0.1103 0.1090 > > . > > 2454 2456 90.0 0.1078 0.1479 0.1090 > > 771 773 48.5 0.1011 0.1012 0.1010 > > .. > > 771 773 39.8 0.1012 0.1005 0.1010 --> *Gly NZ and HZ1, HZ2* > > 771 772 34.9 0.1012 0.1030 0.1010 > > ... > > 2454 2457 102.1 0.1490 38312886396780544. 0.1522 > > 2454 2456 83.0 5.9313 39290317874135040. 0.1090 > > ... > > First errors are with atoms from the residues with *new isopeptide bond*. > I suppose, that this bond is not good. > > > Seems like a reasonable hypothesis - but do look at 2454 and 2456 as well. > You have to get out your trajectory and a visualization package and see what > is actually going wrong. The warnings can be symptomatic of a problem that > started elsewhere. > > You say you've added new interaction types, but I see no reason why you > would need to. It's chemically so similar to a backbone peptide that you may > as well keep things the same and model it the same way. Regardless, you > should probably check that the specbond.dat mechanism has created > interactions that make sense. Compare with a normal peptide bond. > > Mark > > > Please can you advice me how yo make this isopeptide bond good? > > Can I just remove this hydrogens? > > -- > > Sincerely, > > Yulian Gavrilov > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] isopeptide bond
Yes, I checked topol.top. There are all isopeptide bonds ,that I want (according to atom contacts, angles, etc.) 2011/3/13 Mark Abraham > On 13/03/2011 9:53 PM, Yulian Gavrilov wrote: > > Thank you! > > I use the correct “O” in Gly according to .rtp and I checked it with vmd. > There is really a new isopeptide bond. When there is no bond, after > minimization and equilibration, Gly and Lys just close to each other but > they are not connected (in vmd). In my case they are connected (in vmd, > pymol). > > > None of these visualization programs read the topology in your .top file. > They just make guesses based on the geometry of the atoms in the coordinate > file. Anything you see that it guessed is irrelevant. Read your pdb2gmx > output, and go and look at the topology to see what atoms have made a bond. > > Mark > > > When I look on step...pdb, one these residues is exploded (it's atoms are > far from each other outside of the water box). > > > 2011/3/13 Mark Abraham > >> On 13/03/2011 8:55 PM, Yulian Gavrilov wrote: >> >> Dear gmx users, >> >> I just started with gromacs. >> >> Can you help me to find my mistake? I already asked about it, but I did >> not understand what to do exactly in my case. >> >> I try to run to add a new *isopeptide bone* to connect Lys and Gly (to >> make a tetramer of *ubiquitin*). I use AMBER99 force field, Gromacs >> 4.0.5. >> >> What I did: >> >>1. >> >>I changed names of residues according to AMBER rules (LYS to LYN >>etc.). >> 2. >> >>Added new type of residues to ffamber.rtp (LYN -> LYQ and GLY -> GLQ >>that are making a new isopeptide bond) and added a new line to >> specbond.dat >>(LYN NZ 1 GLY C 1 0.13 LYQ GLQ) to make such a bond. >> >> >> IIRC, this creates a bond between the lysine side-chain amine N and >> glycine *backbone* carbonyl C. You must use the atom name for the side-chain >> carbonyl carbon (see .rtp entry for GLY). If you've done this wrong, then >> specbond will probably not have made a bond, because the backbone carbonyl C >> was too far away. You should check your pdb2gmx output carefully. >> >> >> >>1. >> 2. >> >>Added new bond type, angle type and dihedral type to ffamber99bon.itp >> >> >> After running of MD (I've got good minimization and equilibration – nvt >> and npt) I've got such an error: >> >> >> starting mdrun 'Protein in water' >> >> 60 steps, 1200.0 ps. >> >> step 94100, will finish Sun Mar 13 08:15:56 2011 >> >> Step 94124, time 188.248 (ps) LINCS WARNING >> >> relative constraint deviation after LINCS: >> >> rms 0.000796, max 0.032792 (between atoms 2454 and 2456) >> >> bonds that rotated more than 30 degrees: >> >> atom 1 atom 2 angle previous, current, constraint length >> >> 2454 2457 35.6 0.1522 0.1545 0.1522 >> >> >> And after it the same type of errors with another atoms: >> >> 2454 2456 36.1 0.1106 0.1113 0.1090 --> *Gly CA and HA1, HA2* >> >> 2454 2455 40.5 0.1114 0.1103 0.1090 >> >> . >> >> 2454 2456 90.0 0.1078 0.1479 0.1090 >> >> 771 773 48.5 0.1011 0.1012 0.1010 >> >> .. >> >> 771 773 39.8 0.1012 0.1005 0.1010 --> *Gly NZ and HZ1, HZ2* >> >> 771 772 34.9 0.1012 0.1030 0.1010 >> >> ... >> >> 2454 2457 102.1 0.1490 38312886396780544. 0.1522 >> >> 2454 2456 83.0 5.9313 39290317874135040. 0.1090 >> >> ... >> >> First errors are with atoms from the residues with *new isopeptide bond*. >> I suppose, that this bond is not good. >> >> >> Seems like a reasonable hypothesis - but do look at 2454 and 2456 as >> well. You have to get out your trajectory and a visualization package and >> see what is actually going wrong. The warnings can be symptomatic of a >> problem that started elsewhere. >> >> You say you've added new interaction types, but I see no reason why you >> would need to. It's chemically so similar to a backbone peptide that you may >> as well keep things the same and model it the same way. Regardless, you >> should probably check that the specbond.dat mechanism has created >> interactions that make sense. Compare with a normal peptide bond. >> >> Mark >> >> >> Please can you advice me how yo make this isopeptide bond good? >> >> Can I just remove this hydrog
Re: [gmx-users] isopeptide bond
Dear, Mark You asking about this (?): According to ffamber99.atp: amber99_34 14.01000 ; N sp2 nitrogen in amide groups amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) If I don't mix, “N” is used in peptide bond in amber99 and “N3” is used in Lys side chain. That is why I didn't use backbone peptide. *[atoms] and [bonds] section for LYQ and GLQ in topol.top * [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 750 amber99_34 48 LYQ N 748 -0.4157 14.01 ; qtot -5.416 751 amber99_17 48 LYQ H 749 0.2719 1.008 ; qtot -5.144 752 amber99_11 48 LYQ CA 750 -0.07206 12.01 ; qtot -5.216 753 amber99_19 48 LYQ HA 751 0.0994 1.008 ; qtot -5.116 754 amber99_11 48 LYQ CB 752 -0.04845 12.01 ; qtot -5.165 755 amber99_18 48 LYQ HB1 753 0.034 1.008 ; qtot -5.131 756 amber99_18 48 LYQ HB2 754 0.034 1.008 ; qtot -5.097 757 amber99_11 48 LYQ CG 755 0.06612 12.01 ; qtot -5.031 758 amber99_18 48 LYQ HG1 756 0.01041 1.008 ; qtot -5.02 759 amber99_18 48 LYQ HG2 757 0.01041 1.008 ; qtot -5.01 760 amber99_11 48 LYQ CD 758 -0.03768 12.01 ; qtot -5.048 761 amber99_18 48 LYQ HD1 759 0.01155 1.008 ; qtot -5.036 762 amber99_18 48 LYQ HD2 760 0.01155 1.008 ; qtot -5.025 763 amber99_11 48 LYQ CE 761 0.32604 12.01 ; qtot -4.699 764 amber99_28 48 LYQ HE1 762 -0.03358 1.008 ; qtot -4.732 765 amber99_28 48 LYQ HE2 763 -0.03358 1.008 ; qtot -4.766 766 amber99_39 48 LYQ NZ 764 -1.03581 14.01 ; qtot -5.801 767 amber99_17 48 LYQ HZ1 765 0.38604 1.008 ; qtot -5.415 768 amber99_17 48 LYQ HZ2 766 0.38604 1.008 ; qtot -5.029 769 amber99_2 48 LYQ C 767 0.5973 12.01 ; qtot -4.432 770 amber99_41 48 LYQ O 768 -0.5679 16 ; qtot -5 2440 amber99_34 152 GLQ N 2438 -0.4157 14.01 ; qtot -12.42 2441 amber99_17 152 GLQ H 2439 0.2719 1.008 ; qtot -12.14 2442 amber99_11 152 GLQ CA 2440 -0.0252 12.01 ; qtot -12.17 2443 amber99_19 152 GLQ HA1 2441 0.0698 1.008 ; qtot -12.1 2444 amber99_19 152 GLQ HA2 2442 0.0698 1.008 ; qtot -12.03 2445 amber99_2 152 GLQ C 2443 0.5973 12.01 ; qtot -11.43 2446 amber99_41 152 GLQ O 2444 -0.5679 16 ; qtot -12 [ bonds ] ; ai aj funct c0 c1 c2 c3 750 751 1 750 752 1 752 753 1 752 754 1 752 769 1 754 755 1 754 756 1 754 757 1 757 758 1 757 759 1 757 760 1 760 761 1 760 762 1 760 763 1 763 764 1 763 765 1 763 766 1 766 767 1 766 768 1 766 2445 1 769 770 1 769 771 1 2440 2441 1 2440 2442 1 2442 2443 1 2442 2444 1 2442 2445 1 2445 2446 1 -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ffamber99.hdb
Dear gromacs users, Please, can you explain the structure of *ffamber99.hdb *file* *For example, LYN7 11HN-CCA 15HACANCBC 26HBCBCACG 26HGCGCBCD 26HDCDCGCE 26HECECDNZ 23HZNZCECD ** Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] isopeptide bond
Dear Mark, Thank you for your help! Now it works! I made MD without errors. I changed N3 to N, add one additional [angletype] to .itp (HP CT N) and removed one of HZ1 from Lys that participate in isopeptide bond; made appropriate changes in .atp, .hdp, .rtp and specbond.dat. 2011/3/14 Mark Abraham > > > On 14/03/11, *Yulian Gavrilov * wrote: > > Dear, Mark > > You asking about this (?): > > According to ffamber99.atp: > > amber99_34 14.01000 ; N sp2 nitrogen in amide groups > > amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) > > If I don't mix, “N” is used in peptide bond in amber99 and “N3” is used > in Lys side chain. That is why I didn't use backbone peptide. > > > N3 is used in a quaternary amine. N is used in an amide. Atom types are > related to the chemical functional group they are *now* in, not what they > were before a notional peptide condensation. You have an amide, and the > nitrogen in it cannot be protonated. I said that in an email a fortnight > ago. Use normal peptide parameters. > > > *[atoms] and [bonds] section for LYQ and GLQ in topol.top * > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass typeB chargeB massB > > 750 amber99_34 48 LYQ N 748 -0.4157 14.01 ; qtot -5.416 > > 751 amber99_17 48 LYQ H 749 0.2719 1.008 ; qtot -5.144 > > 752 amber99_11 48 LYQ CA 750 -0.07206 12.01 ; qtot -5.216 > > 753 amber99_19 48 LYQ HA 751 0.0994 1.008 ; qtot -5.116 > > 754 amber99_11 48 LYQ CB 752 -0.04845 12.01 ; qtot -5.165 > > 755 amber99_18 48 LYQ HB1 753 0.034 1.008 ; qtot -5.131 > > 756 amber99_18 48 LYQ HB2 754 0.034 1.008 ; qtot -5.097 > > 757 amber99_11 48 LYQ CG 755 0.06612 12.01 ; qtot -5.031 > > 758 amber99_18 48 LYQ HG1 756 0.01041 1.008 ; qtot -5.02 > > 759 amber99_18 48 LYQ HG2 757 0.01041 1.008 ; qtot -5.01 > > 760 amber99_11 48 LYQ CD 758 -0.03768 12.01 ; qtot -5.048 > > 761 amber99_18 48 LYQ HD1 759 0.01155 1.008 ; qtot -5.036 > > 762 amber99_18 48 LYQ HD2 760 0.01155 1.008 ; qtot -5.025 > > 763 amber99_11 48 LYQ CE 761 0.32604 12.01 ; qtot -4.699 > > 764 amber99_28 48 LYQ HE1 762 -0.03358 1.008 ; qtot -4.732 > > 765 amber99_28 48 LYQ HE2 763 -0.03358 1.008 ; qtot -4.766 > > 766 amber99_39 48 LYQ NZ 764 -1.03581 14.01 ; qtot -5.801 > > 767 amber99_17 48 LYQ HZ1 765 0.38604 1.008 ; qtot -5.415 > > 768 amber99_17 48 LYQ HZ2 766 0.38604 1.008 ; qtot -5.029 > > > Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no > such thing as a quaternary amide nitrogen, and certainly AMBER does not have > parameters for it. > > > 769 amber99_2 48 LYQ C 767 0.5973 12.01 ; qtot -4.432 > > 770 amber99_41 48 LYQ O 768 -0.5679 16 ; qtot -5 > > > > 2440 amber99_34 152 GLQ N 2438 -0.4157 14.01 ; qtot -12.42 > > 2441 amber99_17 152 GLQ H 2439 0.2719 1.008 ; qtot -12.14 > > 2442 amber99_11 152 GLQ CA 2440 -0.0252 12.01 ; qtot -12.17 > > 2443 amber99_19 152 GLQ HA1 2441 0.0698 1.008 ; qtot -12.1 > > 2444 amber99_19 152 GLQ HA2 2442 0.0698 1.008 ; qtot -12.03 > > 2445 amber99_2 152 GLQ C 2443 0.5973 12.01 ; qtot -11.43 > > 2446 amber99_41 152 GLQ O 2444 -0.5679 16 ; qtot -12 > > > > [ bonds ] > > ; ai aj funct c0 c1 c2 c3 > > 750 751 1 > > 750 752 1 > > 752 753 1 > > 752 754 1 > > 752 769 1 > > 754 755 1 > > 754 756 1 > > 754 757 1 > > 757 758 1 > > 757 759 1 > > 757 760 1 > > 760 761 1 > > 760 762 1 > > 760 763 1 > > 763 764 1 > > 763 765 1 > > 763 766 1 > > 766 767 1 > > 766 768 1 > > 766 2445 1 > > > OK, you have the N-C bond for the peptide link. > > > 769 770 1 > > 769 771 1 > > > > 2440 2441 1 > > 2440 2442 1 > > 2442 2443 1 > > 2442 2444 1 > > 2442 2445 1 > > 2445 2446 1 > > > Does 2445 make any other bonds? If not, how did you handle the chain > termination? > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] isopeptide bond
Thanks! I understand it, but I had several errors about it. Without adding of (HP CT N) [angletype] it does not work. How to force it to take its type from its current environment, not its historical one? 2011/3/15 Mark Abraham > > > On 15/03/11, *Yulian Gavrilov * wrote: > > Dear Mark, > Thank you for your help! Now it works! I made MD without errors. > I changed N3 to N, add one additional [angletype] to .itp (HP CT N) and > removed one of HZ1 from Lys that participate in isopeptide bond; made > appropriate changes in .atp, .hdp, .rtp and specbond.dat. > > > Good. Like I've said a few times, you have a normal peptide bond and those > interaction types all exist already; you do not need to add more interaction > types. Look up in the .rtp what the HP atom type is used for. The H atom on > the N should take its type from its current environment, not its historical > one. Until your peptide bond resembles a backbone peptide in *all* > particulars, it is not a well-modeled peptide bond. > > Mark > > > 2011/3/14 Mark Abraham > >> >> >> On 14/03/11, *Yulian Gavrilov * wrote: >> >> Dear, Mark >> >> You asking about this (?): >> >> According to ffamber99.atp: >> >> amber99_34 14.01000 ; N sp2 nitrogen in amide groups >> >> amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) >> >> If I don't mix, “N” is used in peptide bond in amber99 and “N3” is used >> in Lys side chain. That is why I didn't use backbone peptide. >> >> >> N3 is used in a quaternary amine. N is used in an amide. Atom types are >> related to the chemical functional group they are *now* in, not what they >> were before a notional peptide condensation. You have an amide, and the >> nitrogen in it cannot be protonated. I said that in an email a fortnight >> ago. Use normal peptide parameters. >> >> >> *[atoms] and [bonds] section for LYQ and GLQ in topol.top * >> >> [ atoms ] >> >> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB >> >> 750 amber99_34 48 LYQ N 748 -0.4157 14.01 ; qtot -5.416 >> >> 751 amber99_17 48 LYQ H 749 0.2719 1.008 ; qtot -5.144 >> >> 752 amber99_11 48 LYQ CA 750 -0.07206 12.01 ; qtot -5.216 >> >> 753 amber99_19 48 LYQ HA 751 0.0994 1.008 ; qtot -5.116 >> >> 754 amber99_11 48 LYQ CB 752 -0.04845 12.01 ; qtot -5.165 >> >> 755 amber99_18 48 LYQ HB1 753 0.034 1.008 ; qtot -5.131 >> >> 756 amber99_18 48 LYQ HB2 754 0.034 1.008 ; qtot -5.097 >> >> 757 amber99_11 48 LYQ CG 755 0.06612 12.01 ; qtot -5.031 >> >> 758 amber99_18 48 LYQ HG1 756 0.01041 1.008 ; qtot -5.02 >> >> 759 amber99_18 48 LYQ HG2 757 0.01041 1.008 ; qtot -5.01 >> >> 760 amber99_11 48 LYQ CD 758 -0.03768 12.01 ; qtot -5.048 >> >> 761 amber99_18 48 LYQ HD1 759 0.01155 1.008 ; qtot -5.036 >> >> 762 amber99_18 48 LYQ HD2 760 0.01155 1.008 ; qtot -5.025 >> >> 763 amber99_11 48 LYQ CE 761 0.32604 12.01 ; qtot -4.699 >> >> 764 amber99_28 48 LYQ HE1 762 -0.03358 1.008 ; qtot -4.732 >> >> 765 amber99_28 48 LYQ HE2 763 -0.03358 1.008 ; qtot -4.766 >> >> 766 amber99_39 48 LYQ NZ 764 -1.03581 14.01 ; qtot -5.801 >> >> 767 amber99_17 48 LYQ HZ1 765 0.38604 1.008 ; qtot -5.415 >> >> 768 amber99_17 48 LYQ HZ2 766 0.38604 1.008 ; qtot -5.029 >> >> >> Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no >> such thing as a quaternary amide nitrogen, and certainly AMBER does not have >> parameters for it. >> >> >> >> 769 amber99_2 48 LYQ C 767 0.5973 12.01 ; qtot -4.432 >> >> 770 amber99_41 48 LYQ O 768 -0.5679 16 ; qtot -5 >> >> >> >> 2440 amber99_34 152 GLQ N 2438 -0.4157 14.01 ; qtot -12.42 >> >> 2441 amber99_17 152 GLQ H 2439 0.2719 1.008 ; qtot -12.14 >> >> 2442 amber99_11 152 GLQ CA 2440 -0.0252 12.01 ; qtot -12.17 >> >> 2443 amber99_19 152 GLQ HA1 2441 0.0698 1.008 ; qtot -12.1 >> >> 2444 amber99_19 152 GLQ HA2 2442 0.0698 1.008 ; qtot -12.03 >> >> 2445 amber99_2 152 GLQ C 2443 0.5973 12.01 ; qtot -11.43 >> >> 2446 amber99_41 152 GLQ O 2444 -0.5679 16 ; qtot -12 >> >> >> >> [ bonds ] >> >> ; ai aj funct c0 c1 c2 c3 >> >> 750 751 1 >> >> 750 752 1 >> >> 752 753 1 >> >> 752 754 1 >> >> 752 769 1 >> >> 754 755 1 >> >> 754 756 1 >> >> 754 757 1 >> >> 757 758 1 >> >> 757 759 1 >> >> 757 760 1 &g
[gmx-users] g_mdmat distance matrices
Dear gmx users, I used g_mdmat and have got a distance matrices in .xpm format. Now I want to compare two matrices: for a protein var1 and for protein var2 and create one output file with this compare. How can I do it? If there is no such function in gromacs, how can I convert .xpm format to get a matrices with numbers? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] average trajectory
Dear gromacs users, 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns). I want to make a distance matrix (*g_mdmat*) for the average trajectory of these 3 runnings. *g_mdmat* gives an average matrix for one trajectory, but I want to get it for the average trajectory. I tried to use *xpm2ps* to get average matrix, but in it I can only combine matrices (not to take an average matrix). Can I get an average matrix, or an average trajectory? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv and g_filter
Dear Gromacs users, What type of conversion of coordinates is better to use? I have got 100 ns MD simulations for unmodified ubc7 protein and ubiquitinated ubc7 protein and converted it's trajectories by using trjconv and g_filter: 1.*trjconv* -s md100ns.tpr -f traj.xtc -o traj_noPBC_nojump.xtc -pbc nojump -ur compact -dt 100 2. *g_filter* -f traj.xtc -s md100ns.tpr -oh highpass.xtc -nojump -b 25000 -dt 100 -fit -n calpha.ndx I tried RMSF analysis for both variants. In *trjconv* there are strange jumps (3, 4.5 angstroms) of residues 21, 45, 100, etc. Most of these residues are within loops. It seems normal, that they move more than others. But 4.5 angstroms – is it ok? As I understand *g_filter* is used more to make good movies, but without it I get strange RMSF. Can I use g_filter instead of using trajconv or after trajconv? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] make a new bond in VERSION 4.5.4
Dear gmx users, I am trying to make a new isopeptide bond between Lys and Gly in VERSION 4.5.4. I did it in VERSION 4.0.5 but can not do it in this version of Gromacs (steps are the same). *In PDB:* ... ATOM 1474 NZ LYN A 93 0.422 60.111 0.829 1.00 1.85 A N ... ATOM 1485 HZ1 LYN A 93 0.848 60.489 1.646 1.00 0.22 A H (only one HZ) Terminal GLY also can be involved to isopeptide bond: ATOM 3827 N GLY B 240 2.191 62.558 -0.381 1.00 1.85 B N ATOM 3828 CA GLY B 240 0.775 62.390 -0.063 1.00 2.17 B C ATOM 3829 C GLY B 240 0.323 60.961 -0.200 1.00 2.00 B C ATOM 3830 O GLY B 240 -0.097 60.559 -1.281 1.00 1.70 B O ATOM 3831 HN GLY B 240 2.551 62.033 -1.148 1.00 0.22 B H ATOM 3832 HA1 GLY B 240 0.209 62.976 -0.771 1.00 1.32 B H ATOM 3833 HA2 GLY B 240 0.599 62.684 0.961 1.00 1.32 B H In Pymol the is a connection (NZ of LYS93_domain_A – 0.13 nm – C of GLY240_domain_B). *I added: * *1) *to ffbonded.itp [ angletypes ] HP CT N 1 109.500 418.400 [ bondtypes ] etc. for ineptitude bond are already exist *2) *to specbond.dat LYSNZ 1GLYC 1 0.13 LYQ GLQ GLQ the same as GLY (originally it should be CGLY, it is C-terminal) LYQ the same as LYN, but only with one HZ1 and [NZ N - 0.64977 17] (instead of NZ N3) *3) *Added LYQ and GLQ to the residuetype.dat (to aminoacids.dat in VERSION 4.0.5) *4) *Added to aminoacids.hdb: LYQ 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG 2 6 HG CG CB CD 2 6 HD CD CG CE 2 6 HE CE CD NZ 1 1 HZ NZ CE CD GLQ – same as GLY *After* pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o processed.gro -water tip3p -chainsep interactive -ignh -rtpres There are no LYQ and GLQ topol.top (instead of it LYS with 3 HZ3 and CGLY) and no bond (residues are not connected after minimization). Force field: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) ___ In VERSION 4.0.5 first I changed names of residues according to Amber (Amber 99) specificity: LYS to LYP and LYN etc. And in specbond.dat it was: LYN NZ 1 GLY C 1 0.13 LYQ GLQ (it works ok) -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make a new bond in VERSION 4.5.4
Thank you! I changed the residue names in the .pdb file to LYQ and GLQ LYQ NZ 1 GLQ C 1 0.13 LYQ GLQ pdb2gmx -f ubc7_94_t48_newgmx1.pdb -o processed.gro -water tip3p -chainsep interactive -ignh -rtpres Program pdb2gmx, VERSION 4.5.4 Source code file: resall.c, line: 581 Fatal error: Residue 'LYQ' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I checked http://www.gromacs.org/Documentation/File_Formats/Topology_File But as you see from the previous mail, I included LYQ and GLQ to the force field. Maybe I missed something? -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make a new bond in VERSION 4.5.4
Dear Justin, gmx users, I forgot to write, but I added these new residues to aminoacids.rtp. Maybe I need to add them also to aminoacids.r2b? How to do it correctly? Just new lines in it or add them to lines of Gly and Lys? So, I suppose it is all steps in http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field [ LYQ ] [ atoms ] N N -0.41570 1 H H 0.27190 2 CA CT -0.07206 3 HA H1 0.09940 4 CB CT -0.04845 5 HB1 HC 0.03400 6 HB2 HC 0.03400 7 CG CT 0.06612 8 HG1 HC 0.01041 9 HG2 HC 0.01041 10 CD CT -0.03768 11 HD1 HC 0.01155 12 HD2 HC 0.01155 13 CE CT 0.32604 14 HE1 HP -0.03358 15 HE2 HP -0.03358 16 NZ N -0.64977 17 HZ1 H 0.38604 18 C C 0.59730 19 O O -0.56790 20 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG CD CD HD1 CD HD2 CD CE CE HE1 CE HE2 CE NZ NZ HZ1 C O -C N [ impropers ] -C CA N H CA +N C O [ GLQ ] [ atoms ] N N -0.41570 1 H H 0.27190 2 CA CT -0.02520 3 HA1 H1 0.06980 4 HA2 H1 0.06980 5 C C 0.59730 6 O O -0.56790 7 [ bonds ] N H N CA CA HA1 CA HA2 CA C C O -C N [ impropers ] -C CA N H CA +N C O -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] make a new bond in VERSION 4.5.4
Dear Justin, gmx users, I putted a FF folder to the gromacs execution directory + changed specbond.dat and it works (I have got isopeptide bond). In old gromacs I needed only to made a local copy of all gromacs and made changes in FF in its folders and not to copy FF folder to execution directory (every time to each new execution directory). Note difference. Maybe I can do somehow the same for new gromacs. Thank you very much for help! You pay a lot of attention for my requests as usual. P.S + to specbond.dat: *LYS* NZ 1 *GLY* C 1 0.13LYQ GLQ -- Sincerely, Yulian Gavrilov -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
