Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan To: "gmx-users@gromacs.org" Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all, I a

RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

Thanks Jianguo,   It doesn't seem to make a difference even if i use -ignh -- I still get the same error.   From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

Not sure what is the problem. but if you have changed the name of the first/last residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to aminoacids.dat file (also change the number in the first line). Cheers, Jianguo From: Kamesh Narasimh

RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

The termini were changed to NXXX/CXXX and the aminoacids.dat file has these two names as well. So nothing very evident.   I can see that there was a thread on precisely this issue --- but how it was resolved is not very evident.   http://www.mail-archive.com/gmx-users@gromacs.org/msg18545.html  

Re: [gmx-users] Regarding xpm2ps

bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also d

Re: [gmx-users] Regarding xpm2ps

Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file fr

Re: [gmx-users] Regarding xpm2ps

bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-ax

[gmx-users] Conversion of gromacs trajectory file

Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Conversion of gromacs trajectory file

aiswarya.pa...@gmail.com wrote: Hello Everyone, Any idea how one can convert gromacs trajectory file to amber file. So as to use the amber tools. The key is finding a compatible intermediate that can be converted. I've found that PDB format is pretty universal. I have a script that does

Re: [gmx-users] Conversion of gromacs trajectory file

Hi Justin, Thank for the quick response. I would try out your script for the conversion. Best, Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Discussion list for GROMACS users ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Conversion of gromacs trajectory f

[gmx-users] Hydrogen existence time

Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Thank you, Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

Re: [gmx-users] Hydrogen existence time

aiswarya.pa...@gmail.com wrote: Dear all, Does Hydrogen bond existence in a time frame states the residence time of the water molecule? Not necessarily, no. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee De

[gmx-users] Convert drug Charmm topology to Gromacs

Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Thanks, Steve -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] Hydrogen existence time

Dear Justin, So what does the hydrogen bond existence state? Thanks --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:54 PM aiswarya.pa...@gmail.com wrote: > Dear

Re: [gmx-users] Convert drug Charmm topology to Gromacs

Steven Neumann wrote: Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Start with Chapter 5 of the manual to understand the required file format

Re: [gmx-users] Hydrogen existence time

aiswarya.pa...@gmail.com wrote: Dear Justin, So what does the hydrogen bond existence state? The length of time for which a given hydrogen bond exists (i.e. satisfies the geometrical criteria in the context of some particular partner group). -Justin Thanks --Original Message--

Re: [gmx-users] Hydrogen existence time

Any idea how can I calculate the residence time of water. Aiswarya --Original Message-- From: Justin A. Lemkul To: Aiswarya Pawar To: Gromacs mail ReplyTo: jalem...@vt.edu Subject: Re: [gmx-users] Hydrogen existence time Sent: 24 Aug 2011 5:58 PM aiswarya.pa...@gmail.com wrote: > Dear J

Re: [gmx-users] Convert drug Charmm topology to Gromacs

On 24/08/2011 10:27 PM, Justin A. Lemkul wrote: Steven Neumann wrote: Dear Gromacs Users, I have generated topology file for CHARMM ff using online server for my small molecule (I obtained .str file). How can I convert it into the Gromacs topology file (.itp)? Start with Chapter 5 of th

Re: [gmx-users] Regarding xpm2ps

Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >

Re: [gmx-users] Hydrogen existence time

aiswarya.pa...@gmail.com wrote: Any idea how can I calculate the residence time of water. There have been recent discussions on this topic, so please check the archive. The solution is an external program that one of the users provided; there are no Gromacs tools that will do this. -Just

Re: [gmx-users] Regarding xpm2ps

bipin singh wrote: Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... Try with "-xmin -5 -5 0 -xmax 5 5 0" - the meaning of the z-

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

It's reading it as GLY tho so maybe you have NGLY in the wrong column? Maybe try move it over one to the right? Oliver On 24 August 2011 09:47, Kamesh Narasimhan wrote: > The termini were changed to NXXX/CXXX and the aminoacids.dat file has > these two names as well. So nothing very evident. >

RE: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

Thanks! that did it. It was the wrong column issue.   However, I can see now that I am getting a non-integer charge for my first nucleic acid chain using the amber03 forcefield. I did replace the aminoacids.dat with the aminoacids-NA.dat contents from the amber port.   How do I overcome this ?

Antw: Re: [gmx-users] Hydrogen existence time

You do not know, what you are doing as I suppose. I suggested you already to calculate the H-bond correlation time, or the self-diffusion coefficient of this specific molecule. >>> "Justin A. Lemkul" 24.08.11 15.04 Uhr >>> aiswarya.pa...@gmail.com wrote: > Any idea how can I calculate the resi

Re: Antw: Re: [gmx-users] Hydrogen existence time

Dear Emanuel, Iam following what you have mentioned earlier. But as you said hydrogen bond correlation time gives the average hydrogen bond existence time. So I confused understanding whether an H Bond existence time would give me the residence time. Aiswarya Sent from my BlackBerry® on Relianc

Re: [gmx-users] Hydrogen existence time

Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0. N(t) index of water molecule found in the hydration sit

Antw: Re: [gmx-users] Hydrogen existence time

As I told you, you can calculate the self-diffusion coefficient by using g_msd. Following: Large diffusion-coeff. --> means : The residence time is low. Small diffusion-coeff. --> means : The residence time is large Mean-square-displacement means: Displacement of molecules per time. No displ

Re: [gmx-users] Convert drug Charmm topology to Gromacs

Hi, The .str file contains the information of atomtype, bonds and improper dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to generate the itp file. And you also need to add the missing parameters from CgenFF into the itp parameter files based on chapter 5, as Justin sug

Re: [gmx-users] Convert drug Charmm topology to Gromacs

Hi, Thank you for the information. Is it easier just to use SwissParam as mentioned and straight obtain itp file for my drug? Steve On Wed, Aug 24, 2011 at 3:57 PM, Jianguo Li wrote: > Hi, > > The .str file contains the information of atomtype, bonds and improper > dihedrals, so it is eneough

Re: Antw: Re: [gmx-users] Hydrogen existence time

Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to small character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Networ

Re: Antw: Re: [gmx-users] Hydrogen existence time

Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. Aiswarya Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network

[gmx-users] gromacs: sound wave in liquid?

Dear all, Sorry if my question sounds irrelevant but I am wondering to know if in gromacs there is any tool for studying properties like sound wave/acoustic wave (An acoustic wave is a pressure oscillation that travels through liquid, in a wave pattern)? I dont see such a tool in the manual but I

Antw: Re: Antw: Re: [gmx-users] Hydrogen existence time

Good luck >>> 24.08.11 18.14 Uhr >>> Emanuel, The residence time which am referring is the water molecule residing on the particular location at a specific time. Am not able to write a correct equation due to some character missing when typing from phone. AiswaryaSent from my BlackBerry® on Re

Re: [gmx-users] Convert drug Charmm topology to Gromacs

Steven Neumann wrote: Hi, Thank you for the information. Is it easier just to use SwissParam as mentioned and straight obtain itp file for my drug? I'd say so. Otherwise you have to go through the trouble of converting it all into the proper format and units. Writing an .rtp entry i

Re: [gmx-users] gromacs: sound wave in liquid?

On Wed, 2011-08-24 at 12:25 -0400, Juliette N. wrote: > Dear all, > > Sorry if my question sounds irrelevant but I am wondering to know if > in gromacs there is any tool for studying properties like sound > wave/acoustic wave (An acoustic wave is a pressure oscillation that > travels through liqui

Re: [gmx-users] Regarding xpm2ps

Sir, Thanks a lot for your help..Its working... On Wed, Aug 24, 2011 at 18:34, Justin A. Lemkul wrote: > > > bipin singh wrote: >> >> Thanks for your kind help, >> I have tried as per your suggestion, the below command >> >> g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm >> >> It is run

[gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule

Hi all, I am trying to build a topology for a synthetic molecule that consists of peptides connected by oligoethyleneglycol (I'll call it PEG) linkers terminated with an amine and a carboxylic acid: -NH2-CH2-[CH2-O-CH2]n-CH2-C(=O)- The system looks like this: N-(PEG)-C-N-(peptide2)-Lys(C-te

[gmx-users] Convert drug Charmm topology to Gromacs

Hello Steven Neumann, I recently converted CGenFF parameters into files that are used by Gromacs. If this is what you need, shoot me an email and I can provide you with the data sets. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723

Re: [gmx-users] gromacs: sound wave in liquid?

On Wed, 24 Aug 2011 12:25:51 -0400 "Juliette N." wrote: > Dear all, > > Sorry if my question sounds irrelevant but I am wondering to know if > in gromacs there is any tool for studying properties like sound > wave/acoustic wave (An acoustic wave is a pressure oscillation that > travels through li

[gmx-users] index file subgroups

Hello, I am trying to figure out how to plot or obtain the average values of Gyration radius from different subgroups of index file. index file prompts for a single group and I need to calculate the averages for all subgroup by hand. Is there any way to compute averages or plot all subgroups dire

Re: [gmx-users] index file subgroups

Elisabeth wrote: Hello, I am trying to figure out how to plot or obtain the average values of Gyration radius from different subgroups of index file. index file prompts for a single group and I need to calculate the averages for all subgroup by hand. Is there any way to compute averages o

[gmx-users] gd_29 or gd_41 ?

Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000 3.77 3 ; -C,CHn,SI- 0.9 ; ... #define gd_41 0.000 3.77 6 ; -CHn-NT-

[gmx-users] Re: gd_29 or gd_41 ?

similarly, why would CA-CB-CG-OD2/1 in ASP be gd_40 instead of gd_34 ? #define gd_34 0.000 5.92 3 ; -CHn,SI-CHn-1.4 ; ... #define gd_40 0.0001.0 6 ; -CHn-C,NR(ring), CR1- 0.24 ; Something wrong with my interpretation of the comments after each d

[gmx-users] sugar dihedral parameters

Hi, In the ATB-distributed 53a6_carbo_new.dat, there are more than one set of parameters specified for some dihedral angles. For example, O5-C5-C6-O6 has a 1-fold term as gd_5, and a 3-fold term gd_37; C3-C2-C1-O5 has a 2-fold term as gd_17, and a 3-fold term as gd_34. So which one should I use

Re: [gmx-users] gd_29 or gd_41 ?

Yun Shi wrote: Hi, For a H-NL-CH1-CH2 (H1-N-CA-C) dihedral angle in a N-terminal MET, why would pdb2gmx automatically assign gd_29 ? In /gromos53a6.ff/ffbonded.itp, it appears: #define gd_29 0.000 3.77 3 ; -C,CHn,SI- 0.9 ; The comment here is incomplete. See the

Re: [gmx-users] Re: gd_29 or gd_41 ?

Yun Shi wrote: similarly, why would CA-CB-CG-OD2/1 in ASP be gd_40 instead of gd_34 ? #define gd_34 0.000 5.92 3 ; -CHn,SI-CHn-1.4 ; ... #define gd_40 0.0001.0 6 ; -CHn-C,NR(ring), CR1- 0.24 ; Something wrong with my interpretation of the co

Re: [gmx-users] sugar dihedral parameters

Yun Shi wrote: Hi, In the ATB-distributed 53a6_carbo_new.dat, there are more than one set of parameters specified for some dihedral angles. For example, O5-C5-C6-O6 has a 1-fold term as gd_5, and a 3-fold term gd_37; C3-C2-C1-O5 has a 2-fold term as gd_17, and a 3-fold term as gd_34. So w

Re: [gmx-users] Hydrogen existence time

On 25/08/2011 12:00 AM, aiswarya.pa...@gmail.com wrote: Mark, The residence time equation goes like this- P(r)= function (N(t) - N(t+r))dt Where function(x-y) takes the value of 1 when x=y(x not equal to 0 and y not equal to 0) ie the site occupied and when x not equal to y or both x and y =0

[gmx-users] surface area calculations for MARTINI

Hi, I'm trying to do some surface area calculations on MARTINI models using APBS, which requires supplying vdw radii via a pqr file. Given how MARTINI treats LJ interactions (0.47 nm radius for all particle types), how do I calculate reasonable effective vdw radii? Obviously the PC headgroup (NC3