[gmx-users] A common error Atom O11 in residue bDM 1 was
You are right Justin, The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why this problem happens ? Should I change the name of these atoms in the rtp and pdb files ? Is a trick is available to avoid this "bad" translation ? Stefane ABEL Stephane 175950 wrote: > Dear all, > > I have a very "common" problem when I try to convert a pdb file to a gro file > with the following command. > > I use charmm27ff and gmx4.5.1. > > pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp > > I obtain the following "commun" error : > > "Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms while > sorting atoms". > > I am surprised to have this message, since after verification in the > 1-bDM.pdb, I have not found an atom with this name. I have also checked the > format of the pdb and all the fields are in right place. > Probably atom 1O1 is being translated as O11. I have had similar problems with translated atom names. If you add "-debug 1" to your pdb2gmx command line, you will get output .pdb files containing the structure as pdb2gmx is interpreting it. That's how I've identified some spurious translations before. -Justin > Below my PDB file > ATOM 1 1C1 bDM 1 -28.807 -8.973 -4.361 0.30 0.00 > ATOM 2 H1A bDM 1 -28.976 -9.551 -3.427 0.10 0.00 > ATOM 3 1O1 bDM 1 -27.541 -9.232 -4.796 -0.40 0.00 > ATOM 4 1C2 bDM 1 -29.836 -9.352 -5.325 0.14 0.00 > ATOM 5 H2A bDM 1 -30.783 -9.324 -4.746 0.09 0.00 > ATOM 6 1O2 bDM 1 -29.680 -10.694 -5.733 -0.66 0.00 > ATOM 7 H2OA bDM 1 -28.731 -10.800 -5.827 0.43 0.00 > ATOM 8 1C3 bDM 1 -29.990 -8.385 -6.493 0.14 0.00 > ATOM 9 H3A bDM 1 -29.086 -8.411 -7.139 0.09 0.00 > ATOM 10 1O3 bDM 1 -31.239 -8.585 -7.237 -0.66 0.00 > ATOM 11 H3OA bDM 1 -31.193 -8.053 -8.035 0.43 0.00 > ATOM 12 1C4 bDM 1 -29.957 -6.922 -6.018 0.14 0.00 > ATOM 13 H4A bDM 1 -30.923 -6.772 -5.490 0.09 0.00 > ATOM 14 1O4 bDM 1 -29.963 -6.003 -7.122 -0.66 0.00 > ATOM 15 H4OA bDM 1 -29.993 -5.118 -6.751 0.43 0.00 > ATOM 16 1C5 bDM 1 -28.865 -6.650 -5.081 0.10 0.00 > ATOM 17 H5A bDM 1 -27.963 -7.009 -5.622 0.10 0.00 > ATOM 18 1C6 bDM 1 -28.730 -5.254 -4.552 0.05 0.00 > ATOM 19 H61A bDM 1 -29.694 -5.009 -4.056 0.09 0.00 > ATOM 20 H61B bDM 1 -28.509 -4.622 -5.438 0.09 0.00 > ATOM 21 1O6 bDM 1 -27.593 -5.254 -3.684 -0.66 0.00 > ATOM 22 H6OA bDM 1 -27.699 -5.900 -2.982 0.43 0.00 > ATOM 23 1O5 bDM 1 -28.979 -7.582 -3.963 -0.40 0.00 > ATOM 24 2C1 bDM 1 -23.620 -9.286 -3.000 0.20 0.00 > ATOM 25 H1B bDM 1 -23.440 -10.274 -3.475 0.09 0.00 > ATOM 26 2C2 bDM 1 -24.806 -9.283 -2.026 0.14 0.00 > ATOM 27 H2B bDM 1 -24.867 -8.235 -1.662 0.09 0.00 > ATOM 28 2O2 bDM 1 -24.477 -10.097 -0.884 -0.66 0.00 > ATOM 29 H2OB bDM 1 -23.792 -9.775 -0.294 0.43 0.00 > ATOM 30 2C3 bDM 1 -26.163 -9.642 -2.661 0.14 0.00 > ATOM 31 H3B bDM 1 -26.142 -10.663 -3.098 0.09 0.00 > ATOM 32 2O3 bDM 1 -27.232 -9.397 -1.722 -0.66 0.00 > ATOM 33 H3OB bDM 1 -27.384 -10.156 -1.155 0.43 0.00 > ATOM 34 2C4 bDM 1 -26.364 -8.872 -3.987 0.10 0.00 > ATOM 35 H4B bDM 1 -26.533 -7.835 -3.626 0.10 0.00 > ATOM 36 2C5 bDM 1 -25.089 -8.936 -4.892 0.25 0.00 > ATOM 37 H5B bDM 1 -24.906 -9.942 -5.326 0.09 0.00 > ATOM 38 2C6 bDM 1 -25.225 -7.980 -6.074 0.05 0.00 > ATOM 39 H62A bDM 1 -25.159 -6.910 -5.780 0.09 0.00 > ATOM 40 H62B bDM 1 -26.236 -8.045 -6.532 0.09 0.00 > ATOM 41 2O5 bDM 1 -24.218 -8.289 -7.105 -0.66 0.00 > ATOM 42 H5OB bDM 1 -24.661 -8.895 -7.704 0.43 0.00 > ATOM 43 2O4 bDM 1 -24.011 -8.432 -4.077 -0.40 0.00 > ATOM 44 2O1 bDM 1 -22.364 -8.895 -2.386 -0.30 0.00 > ATOM 45 C7 bDM 1 -21.159 -9.105 -3.148 -0.11 0.00 > ATOM 46 H7A bDM 1 -20.922 -10.188 -3.228 0.09 0.00 > ATOM 47 H7B bDM 1 -21.320 -8.848 -4.217 0.09 0.00 > ATOM 48 C8 bDM 1 -19.961 -8.389 -2.410 -0.18 0.00 > ATOM 49 H8A bDM 1 -19.829 -8.778 -1.378 0.09 0.00 > ATOM 50 H8B bDM 1 -20.171 -7.300 -2.464 0.09 0.00 > ATOM 51 C9 bDM 1 -18.547 -8.641 -3.005 -0.18 0.00 > ATOM 52 H9A bDM 1 -18.718 -8.465 -4.089 0.09 0.00 > ATOM 53 H9B bDM 1 -18.415 -9.744 -3.010 0.09 0.00 > ATOM 54 C10 bDM 1 -17.452 -7.785 -2.397 -0.18 0.00 > ATOM 55 H10A bDM 1 -16.675 -7.915 -3.
Re: [gmx-users] A common error Atom O11 in residue bDM 1 was
ABEL Stephane 175950 wrote:
You are right Justin,
The 1O1 atoms and (others 1O2, etc.) are changed to O11, O21, etc. (?). Why
this problem happens ? Should I change the name of these atoms in the rtp and
pdb files ? Is a trick is available to avoid this "bad" translation ?
The only option is to not use digits as the first characters in an atom name.
The code in pdb2gmx.c calls a function "rename_atoms" in xlate.c, which (since a
value of TRUE is passed to the function for bReorderNum), shifts the position of
all digits in the first position:
if (bReorderNum)
{
if (isdigit(atombuf[0]))
{
c = atombuf[0];
for (i=0; ((size_t)iI think the purpose is really to deal with hydrogens (i.e. 1HG1, etc) but
affects all atoms, as written. A check could probably be implemented to
determine if the atom is H or not, but really might not be worth the effort,
since the vast majority of all structures that will be passed to pdb2gmx will
follow the normal route of: character first, then digits.
-Justin
Stefane
ABEL Stephane 175950 wrote:
Dear all,
I have a very "common" problem when I try to convert a pdb file to a gro
file with the following command.
I use charmm27ff and gmx4.5.1.
pdb2gmx_mpi -f 1-bDM.pdb -o 1-bDM.gro -p 1-bDM.top -chargegrp
I obtain the following "commun" error :
"Atom O11 in residue bDM 1 was not found in rtp entry bDM with 80 atoms
while sorting atoms".
I am surprised to have this message, since after verification in the
1-bDM.pdb, I have not found an atom with this name. I have also checked the
format of the pdb and all the fields are in right place.
Probably atom 1O1 is being translated as O11. I have had similar problems
with translated atom names. If you add "-debug 1" to your pdb2gmx command
line, you will get output .pdb files containing the structure as pdb2gmx is
interpreting it. That's how I've identified some spurious translations
before.
-Justin
Below my PDB file ATOM 1 1C1 bDM 1 -28.807 -8.973 -4.361
0.30 0.00 ATOM 2 H1A bDM 1 -28.976 -9.551 -3.427 0.10
0.00 ATOM 3 1O1 bDM 1 -27.541 -9.232 -4.796 -0.40 0.00
ATOM 4 1C2 bDM 1 -29.836 -9.352 -5.325 0.14 0.00 ATOM
5 H2A bDM 1 -30.783 -9.324 -4.746 0.09 0.00 ATOM 6 1O2
bDM 1 -29.680 -10.694 -5.733 -0.66 0.00 ATOM 7 H2OA bDM
1 -28.731 -10.800 -5.827 0.43 0.00 ATOM 8 1C3 bDM 1
-29.990 -8.385 -6.493 0.14 0.00 ATOM 9 H3A bDM 1 -29.086
-8.411 -7.139 0.09 0.00 ATOM 10 1O3 bDM 1 -31.239 -8.585
-7.237 -0.66 0.00 ATOM 11 H3OA bDM 1 -31.193 -8.053 -8.035
0.43 0.00 ATOM 12 1C4 bDM 1 -29.957 -6.922 -6.018 0.14
0.00 ATOM 13 H4A bDM 1 -30.923 -6.772 -5.490 0.09 0.00
ATOM 14 1O4 bDM 1 -29.963 -6.003 -7.122 -0.66 0.00 ATOM
15 H4OA bDM 1 -29.993 -5.118 -6.751 0.43 0.00 ATOM 16 1C5
bDM 1 -28.865 -6.650 -5.081 0.10 0.00 ATOM 17 H5A bDM
1 -27.963 -7.009 -5.622 0.10 0.00 ATOM 18 1C6 bDM 1
-28.730 -5.254 -4.552 0.05 0.00 ATOM 19 H61A bDM 1 -29.694
-5.009 -4.056 0.09 0.00 ATOM 20 H61B bDM 1 -28.509 -4.622
-5.438 0.09 0.00 ATOM 21 1O6 bDM 1 -27.593 -5.254 -3.684
-0.66 0.00 ATOM 22 H6OA bDM 1 -27.699 -5.900 -2.982 0.43
0.00 ATOM 23 1O5 bDM 1 -28.979 -7.582 -3.963 -0.40 0.00
ATOM 24 2C1 bDM 1 -23.620 -9.286 -3.000 0.20 0.00 ATOM
25 H1B bDM 1 -23.440 -10.274 -3.475 0.09 0.00 ATOM 26 2C2
bDM 1 -24.806 -9.283 -2.026 0.14 0.00 ATOM 27 H2B bDM
1 -24.867 -8.235 -1.662 0.09 0.00 ATOM 28 2O2 bDM 1
-24.477 -10.097 -0.884 -0.66 0.00 ATOM 29 H2OB bDM 1 -23.792
-9.775 -0.294 0.43 0.00 ATOM 30 2C3 bDM 1 -26.163 -9.642
-2.661 0.14 0.00 ATOM 31 H3B bDM 1 -26.142 -10.663 -3.098
0.09 0.00 ATOM 32 2O3 bDM 1 -27.232 -9.397 -1.722 -0.66
0.00 ATOM 33 H3OB bDM 1 -27.384 -10.156 -1.155 0.43 0.00
ATOM 34 2C4 bDM 1 -26.364 -8.872 -3.987 0.10 0.00 ATOM
35 H4B bDM 1 -26.533 -7.835 -3.626 0.10 0.00 ATOM 36 2C5
bDM 1 -25.089 -8.936 -4.892 0.25 0.00 ATOM 37 H5B bDM
1 -24.906 -9.942 -5.326 0.09 0.00 ATOM 38 2C6 bDM 1
-25.225 -7.980 -6.074 0.05 0.00 ATOM 39 H62A bDM 1 -25.159
-6.910 -5.780 0.09 0.00 ATOM 40 H62B bDM 1 -26.236 -8.045
-6.532 0.09 0.00 ATOM 41 2O5 bDM 1 -24.218 -8.289 -7.105
-0.66 0.00 ATOM 42 H5OB bDM 1 -24.661 -8.895 -7.704 0.43
0.00 ATOM 43 2O4 bDM 1 -24.011 -8.432 -4.077 -0.40 0.00
ATOM 44 2O1 bDM 1 -22.364 -8.895 -2.386 -0.30 0.00 ATOM
45 C7 bDM 1 -21.159 -9.105 -3.148 -0.11 0.00 ATOM 46 H7A
bDM 1
[gmx-users] About COM pulling
Hi all, I am using GMX4.5.1 to do COM pulling . ; COM PULLING ; Pull type: no, umbrella, constraint or constant_forcepull = umbrella; Pull geometry: distance, direction, cylinder or positionpull_geometry = direction; Select components for the pull vector. default: Y Y Ypull_dim = N N Y; Cylinder radius for dynamic reaction force groups (nm)pull_r1 = 1; Switch from r1 to r0 in case of dynamic reaction forcepull_r0 = 1pull_constr_tol = 1e-06pull_start = yespull_nstxout = 10pull_nstfout = 1; Number of pull groups pull_ngroups = 1; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)pull_group0 = referpull_weights0 = pull_pbcatom0 = 0pull_group1 = Kpull_weights1 = pull_pbcatom1 = 0pull_vec1 = 0.0 0.0 1.0pull_init1 = 0.0pull_rate1 = 0.001pull_k1 = 1000pull_kB1 = I don't know why it did not pull in Z direction? And what does pull_start = yes mean?Thanks !Zhongjin He -- 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] About COM pulling
zhongjin wrote: Hi all, I am using GMX4.5.1 to do COM pulling . ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = umbrella ; Pull geometry: distance, direction, cylinder or position pull_geometry= direction ; Select components for the pull vector. default: Y Y Y pull_dim = N N Y ; Cylinder radius for dynamic reaction force groups (nm) pull_r1 = 1 ; Switch from r1 to r0 in case of dynamic reaction force pull_r0 = 1 pull_constr_tol = 1e-06 pull_start = yes pull_nstxout = 10 pull_nstfout = 1 ; Number of pull groups pull_ngroups = 1 ; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2) pull_group0 = refer pull_weights0= pull_pbcatom0= 0 pull_group1 = K pull_weights1= pull_pbcatom1= 0 pull_vec1= 0.0 0.0 1.0 pull_init1 = 0.0 pull_rate1 = 0.001 pull_k1 = 1000 pull_kB1 = I don't know why it did not pull in Z direction? And what does pull_start = yes mean? You may not be getting a large displacement because you have a slow pulling rate (0.001 nm/ps). There's nothing wrong with it, but if you're running a rather short simulation, that may be insufficient to cause noticeable displacement, depending on the forces that your pull group is experiencing. Please refer to the manual for the interpretation of pull_start (and any other settings, for that matter). http://manual.gromacs.org/current/online/mdp_opt.html#pull All of these settings are also described in the COM pulling tutorial. http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin Thanks ! Zhongjin He -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] electrostatics with non-periodic system
Hi all, Could anybody please suggest "a good method" for electrostatics for non-periodic system simulation -> PBC=no ? Let's say it is pure water system. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- 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] vanadium non-bonded parameters
See Manual, 5.3.3 Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Gonçalo C. Justino > Sent: Saturday, 25 September 2010 5:21 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] vanadium non-bonded parameters > > Dear gmx'ers, > > Does anyone know of any (published or not) non-bonded parameters for > vanadium species for any of the forcefields implemented in GROMACS ? > > If not, my question is: what is the meaning of the null values for > sigma and epsilon in, e.g., amber03, for Fe: > > FE 26 55.000. A 0.0e+00 0.0e+00 > [from the ffnonbonded.itp file] > > Thks for any help, > Gonçalo > -- > 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
[gmx-users] How to make a lipid bilayer with specific dimensions?
Dear gmxusers, I am trying to make a lipid bilayer with specific dimensions using gromacs. So far, I have got up to: 1) Download a lipid POPC128a.pdb from Peter Tieleman's website 2) Use genconf -f popc128a.pdb -o popcx2.pdb -nbox 2 2 1 to multiply the lipid in the x and y axis. The resultant output was a lipid with box vectors 12.478 , 12.359 and 6.919 (nm) My ultimate aim is to generate a POPC bilayer with the dimensions 9.600 9.500 and 14.000. Currently, the lipid bilayer is too big. I would like to "crop" the excess lipids to the required size if at all possible. I tried using editconf ( a bit of a long shot) to make a new box size. The new structure file has a CRYST1 of 9.600 9.500 and 14.000 but when I view it with VMD, it is not any smaller than before. Do I have to use other software to achieve this? If so, I'd really appreciate some pointers. Thanks! << Email has been scanned for viruses by UNMC email management service >> -- 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] Query regarding protonation and deprotonation of some residues
Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostatic interaction with the substrate while carrying out molecular dynamics simulation. It will be appreciable, if you could help me regarding the same, how to deprotonate Tyr and Ser residue and protonate Lysine residue of the protein while preparing the protein topology to be used for molecular dynamics simulation in Gromacs. Thanks and Regards. -- Sonali Dhindwal -- 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] Query regarding protonation and deprotonation of some residues
Hi, You need to define the protonation sate vie pdb2gmx. pdb2gmx -tyr -lys On 27/09/10 2:34 PM, sonali dhindwal wrote: Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostatic interaction with the substrate while carrying out molecular dynamics simulation. It will be appreciable, if you could help me regarding the same, how to deprotonate Tyr and Ser residue and protonate Lysine residue of the protein while preparing the protein topology to be used for molecular dynamics simulation in Gromacs. Thanks and Regards. -- Sonali Dhindwal -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -- 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] Reg: Adding multiple molecules
Hi all I have a diffculty in adding multiple molecules of hexane to my box. my box size is 4.72*2.36*2.36 (nm) according to my number density calculations the box should fit 124 molecules of hexane whereas it adds only 76 molecules to the box below is my command. i had evev tried with -try command but without sucess. genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o hexane-multi.gro -nmol 124 -seed 1268 Regards Vinoth -- 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] electrostatics with non-periodic system
Hi, For pure water (no ions, no external electric field), reaction field does fine even with a short cut-off, e.g. 0.9 nm (use reaction-field-zero if you need good energy conservation). In case you have long-range fields, use no-cutoff at all (all cut-off to 0 in the mdp file) when you system is not too big. You can also embed your system in a large box, something like 3 times larger in all dimensions than your original system and use PME. Berk > From: vvcha...@gmail.com > Date: Sun, 26 Sep 2010 13:03:31 -0400 > To: gmx-users@gromacs.org > Subject: [gmx-users] electrostatics with non-periodic system > > Hi all, > > Could anybody please suggest "a good method" for electrostatics for > non-periodic system simulation -> PBC=no ? Let's say it is pure water > system. > > -- > Dr. Vitaly V. Chaban > Department of Chemistry > University of Rochester > Rochester, NY 14627-0216 > United States of America > -- > 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
Re: [gmx-users] Query regarding protonation and deprotonation of some residues
Thanks Kass for the help. I want to specifically protonate one of the lysine near the active site and deprotonate Tyr and Ser. It will be kind if you can please help me to know how to select that specific residue number. Regards -- Sonali Dhindwal --- On Mon, 27/9/10, Itamar Kass wrote: From: Itamar Kass Subject: Re: [gmx-users] Query regarding protonation and deprotonation of some residues To: "Discussion list for GROMACS users" Date: Monday, 27 September, 2010, 10:07 AM Hi, You need to define the protonation sate vie pdb2gmx. pdb2gmx -tyr -lys On 27/09/10 2:34 PM, sonali dhindwal wrote: Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostatic interaction with the substrate while carrying out molecular dynamics simulation. It will be appreciable, if you could help me regarding the same, how to deprotonate Tyr and Ser residue and protonate Lysine residue of the protein while preparing the protein topology to be used for molecular dynamics simulation in Gromacs. Thanks and Regards. -- Sonali Dhindwal -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu -Inline Attachment Follows- -- gmx-users mailing list gmx-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
