[gmx-users] HEME-cysteine gromacs simulation

You always need a correct topology. The main issue here is that you need to have correct parameters. Where did you get your heme and Fe parameters? Were you careful about the Fe state oxidation state? I suspect that most people use Amber because of their antechamber program, which seems lik

Re: [gmx-users] HEME-cysteine gromacs simulation

?? wrote: HI all: I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topolog

Re: [gmx-users] error while executing grompp

Justin A. Lemkul wrote: Your ffcharmm.itp file lacks a necessary line at the very top: #define _FF_CHARMM Without this line, grompp does not know which force field you are using, and hence everything breaks down when other .itp files are called. On closer inspection, Chanchal's source at h

[gmx-users] HEME-cysteine gromacs simulation

HI all: I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then to construct a correct topology. I read lots o

Re: [gmx-users] error while executing grompp

Chanchal wrote: Hi Justin, I have corrected the ffcharmm.itp file. But I am still getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Generated 0 of the 595 non-bonded parameter combinations ---

Re: [gmx-users] genion question

Paymon Pirzadeh wrote: Well, if I have understood your words properly, apparently there is a problem in the first residue in amino terminal which I treated the NH2 as a zwitterionic piece(+1), and gave the side chain -1 charge. I thought it should add up to zero, but apparently it does not:

Re: [gmx-users] genion question

Well, if I have understood your words properly, apparently there is a problem in the first residue in amino terminal which I treated the NH2 as a zwitterionic piece(+1), and gave the side chain -1 charge. I thought it should add up to zero, but apparently it does not: 1 opls_287 1ASP

Re: [gmx-users] error while executing grompp

Hi Justin, I have corrected the ffcharmm.itp file. But I am still getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Generated 0 of the 595 non-bonded parameter combinations -

Re: [gmx-users] error while executing grompp

Chanchal wrote: Hi Justin, Sorry, I attached the wrong file. Attached is the correct file. There is a space after #define: #define _FF_CHARMM Your file has #define_FF_CHARMM. -Justin Thanks Chanchal On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul > wrote:

Re: [gmx-users] error while executing grompp

Hi Justin, Sorry, I attached the wrong file. Attached is the correct file. Thanks Chanchal On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul wrote: > > > Chanchal wrote: > >> Hi Justin, >> I am still getting the error message : Back Off! I just backed up >> mdout.mdp to ./#mdout.mdp.2# >> ch

Re: [gmx-users] error while executing grompp

Chanchal wrote: Hi Justin, I am still getting the error message : Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Generated 0 of the 595 non-bonded parameter combinations -

Re: [gmx-users] error while executing grompp

Hi Justin, I am still getting the error message : Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Generated 0 of the 595 non-bonded parameter combinations --- Program gro

Re: [gmx-users] genion question

Paymon Pirzadeh wrote: Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including

Re: [gmx-users] make_ndx help

parthi...@ncbs.res.in wrote: Hi Anyone can please tell how to index 2 or more groups using make_ndx eg: 1 protein 12 sol 13 NA+ i tried giving >1&12, which shows that the "Group is empty" Type "help" at the make_ndx prompt; you will see a number of examples. There are also more exa

Re: [gmx-users] make_ndx help

1|12 merges the two groups into a new group (1&12 will merge into a new group any atoms which are in both groups 1 and 12, of which there are none in this case) Tom --On Wednesday, August 26, 2009 04:07:20 +0530 parthi...@ncbs.res.in wrote: Hi Anyone can please tell how to index 2 or more

[gmx-users] make_ndx help

Hi Anyone can please tell how to index 2 or more groups using make_ndx eg: 1 protein 12 sol 13 NA+ i tried giving >1&12, which shows that the "Group is empty" thanks in advance Parthiban ___ gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] error while executing grompp

Your ffcharmm.itp file lacks a necessary line at the very top: #define _FF_CHARMM Without this line, grompp does not know which force field you are using, and hence everything breaks down when other .itp files are called. -Justin Chanchal wrote: Hi, Attached are the top and itp file I am

Re: [gmx-users] genion question

Well, when I look into my .top file, almost no where I see closeness to an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91 sometimes. But I can not see a clear trend on where things go wrong. My protein has only 37 amino acids with 451 atoms (including hydrogens). I am not sure

Re: [gmx-users] genion question

Paymon Pirzadeh wrote: Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the No, it's not. It's NA+. From ions.it

Re: [gmx-users] genion question

Thanks for the tips! But I still have problem with my added ion. Justin had told me that ion names are force-field specific! Since I am using OPLSaa, I checked the itp file for Na ion name, and it was Na+. I used this name with the -pname switch, but again during the grompp I ran into the following

Re: [gmx-users] Mdrun error

Cíntia C. Vequi-Suplicy wrote: Hello Justin, I used Gromacs 4.0.5 and the error was gone. Thank you. But now I have another problem when using mdrun_d. I gave the comand: mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log & And first I got a lot of output on the shell window and

[gmx-users] Re: Mdrun error

Cíntia C. Vequi-Suplicy wrote: Hello Justin, I used Gromacs 4.0.5 and the error was gone. Thank you. But now I have another problem when using mdrun_d. I gave the comand: mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log & And first I got a lot of output on the shell window an

Re: [gmx-users] genion question

Paymon Pirzadeh wrote: Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? It's probably irrelevant. The representation of "decimal" numbers on computers can be inexact, such that things like 0.02 added to itself

[gmx-users] Mdrun error

Hello Justin, I used Gromacs 4.0.5 and the error was gone. Thank you. But now I have another problem when using mdrun_d. I gave the comand: mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log & And first I got a lot of output on the shell window and I think it is strange. This out

Re: [gmx-users] error while executing grompp

Chanchal wrote: Hi All, I have downloaded pdb file and required .top and .itp file from the site http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I execute the command grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e ener.edr -t traj.trr I got the error " Fa

Re: [gmx-users] genion question

Can I change the charge of Na ion added from +1 to +0.99 to cancel the negative charge exactly? Does that hurt science or simulation? Payman On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote: > > Paymon Pirzadeh wrote: > > I realized sth about the previous error message I posted. In th

Re: [gmx-users] error while executing grompp

Chanchal wrote: Hi All, I have downloaded pdb file and required .top and .itp file from the site http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I execute the command grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e ener.edr -t traj.trr I got the error

[gmx-users] error while executing grompp

Hi All, I have downloaded pdb file and required .top and .itp file from the site http://www.bioinf.uni-sb.de/RB/ for DOPC simulation. Now when I execute the command grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal error: [ file

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: I realized sth about the previous error message I posted. In the following I have copied the lines (with their line number) which grompp gives warning on! in .gro file: 65868 10940SOLHW265866 5.038 5.739 6.407 65869 10940SOL MW65867 5.103 5.710 6.4

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

I realized sth about the previous error message I posted. In the following I have copied the lines (with their line number) which grompp gives warning on! in .gro file: 65868 10940SOLHW265866 5.038 5.739 6.407 65869 10940SOL MW65867 5.103 5.710 6.455 65870 10940SOLLP16586

[gmx-users] grompp warning with ion's name

After adding the Na ion, grompp gives the following error: processing coordinates... Warning: atom name 65870 in AFP_I.top and AFP_I_solvated_54_62_102_null.gro does not match (NA - Na) WARNING 1 [file AFP_I.top, line 4151]: 1 non-matching atom name atom names from AFP_I.top will be used a

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: When I look at the .top file generated by pdb2gmx, the last lines show how this -0.99 is generated: 442 opls_302 37ARG CZ138 0.64 12.011 ; qtot -0.33 443 opls_300 37ARGNH1139 -0.814.0067 ; qtot -1.13 44

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

When I look at the .top file generated by pdb2gmx, the last lines show how this -0.99 is generated: 442 opls_302 37ARG CZ138 0.64 12.011 ; qtot -0.33 443 opls_300 37ARGNH1139 -0.814.0067 ; qtot -1.13 444 opls_301 37ARG

Re: [gmx-users] Pressure swings during preliminary runs

Warren Gallin wrote: Justin, OK, I see what's going on. So then, since the instantaneous pressure values are so variable, is there a reason to implement pressure coupling for an MD run? I guess if you're skeptical, check out the references for the coupling algorithms implemented

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: OK! It worked! Thanks a lot again. But I have a final technical question. After running grompp, it shows that my box has a net charge of -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is OK?! or even this 0.01 charge will cause me troubles? Dependi

Re: [gmx-users] Pressure swings during preliminary runs

Justin, OK, I see what's going on. So then, since the instantaneous pressure values are so variable, is there a reason to implement pressure coupling for an MD run? Warren On 25-Aug-09, at 1:23 PM, Justin A. Lemkul wrote: Warren Gallin wrote: HI, I am trying to simulate the

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

OK! It worked! Thanks a lot again. But I have a final technical question. After running grompp, it shows that my box has a net charge of -0.99 . Do you think adding one Na+ and reducing the charge to +0.01 is OK?! or even this 0.01 charge will cause me troubles? Sorry for tons of e-mails. regards,

Re: [gmx-users] Pressure swings during preliminary runs

Warren Gallin wrote: HI, I am trying to simulate the behavior of short peptides in an aqueous solution. When I look at the log of the progress of initial minimization runs and longer production runs I am seeing crazy variations in the pressure, including negative values and positi

[gmx-users] Pressure swings during preliminary runs

HI, I am trying to simulate the behavior of short peptides in an aqueous solution. When I look at the log of the progress of initial minimization runs and longer production runs I am seeing crazy variations in the pressure, including negative values and positive values well into the 1

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Thanks! I had misunderstood you! I thought you meant to modify them in the root directory! My mistake! Thanks a lot. I will try to see what I can do. Payman On Tue, 2009-08-25 at 14:38 -0400, Justin A. Lemkul wrote: > > Paymon Pirzadeh wrote: > > OK! That's fine. But what if I do not have perm

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: OK! That's fine. But what if I do not have permissions to make such changes in the itp files? Also, isn't that the case that when you define That's why I said copy the force field files into your local directory. Once there, you can modify them. sth for the second

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

OK! That's fine. But what if I do not have permissions to make such changes in the itp files? Also, isn't that the case that when you define sth for the second time, grompp will take the second one? Sorry for mass of e-mail! Payman On Tue, 2009-08-25 at 14:26 -0400, Justin A. Lemkul wrote: > >

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: I have done that already! I use my local copy to make my files. but how can I get rid of this error? get into the oplsaanb.itp or include this water model in the topology file before oplsaa.itp? I don't understand what you're saying you've already done. The problem is

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

I have done that already! I use my local copy to make my files. but how can I get rid of this error? get into the oplsaanb.itp or include this water model in the topology file before oplsaa.itp? Payman On Tue, 2009-08-25 at 14:14 -0400, Justin A. Lemkul wrote: > > Paymon Pirzadeh wrote: >

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: OK! here is the .itp file which I generated. I might upload it because it has passed the initial tests. ; This is an itp file to describe water's six-site model by H. Nada and J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003) ; This model is

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

OK! here is the .itp file which I generated. I might upload it because it has passed the initial tests. ; This is an itp file to describe water's six-site model by H. Nada and J.P. J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401-7413 (2003) ; This model is a combination of TIP4P and T

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Paymon Pirzadeh wrote: Hello, Just a reminder that I had troubled with combination rules between my water model and GROMACS forcefields. I fixed the problem by adjusting my water model's parameters. BUT, now, I specified the new parameters in my .itp file under [ atomtype ] category and grompp

Re: [gmx-users] pdb2gmx -water-> grompp; grompp error

Hello, Just a reminder that I had troubled with combination rules between my water model and GROMACS forcefields. I fixed the problem by adjusting my water model's parameters. BUT, now, I specified the new parameters in my .itp file under [ atomtype ] category and grompp makes errors out of the ord

Re: [gmx-users] Grompp error

Cíntia C. Vequi-Suplicy wrote: Hello, I am trying to simulate a lipid membrane with Gromacs. I am trying to generate the *.tpr file o run the simulation, but every time I use the command grompp I got the following error: checking input for internal consistency... ...ling /usr/bin/cpp : No suc

[gmx-users] Grompp error

Hello, I am trying to simulate a lipid membrane with Gromacs. I am trying to generate the *.tpr file o run the simulation, but every time I use the command grompp I got the following error: checking input for internal consistency... ...ling /usr/bin/cpp : No such file or directory cpp exit code:

[gmx-users] QM/MM tutorial available?

Dear Gromacs users, Is there any QM/MM tutorials for gromacs 3.3.3 or 4.0.5 available on line? I cannot find any tutorials that run smoothly with either 3.3.3 or 4.0.5. Thank you in advance. Ye MEI ___ gmx-users mailing listgmx-users@gromacs.org h

[gmx-users] Re: Regarding Gromacs problem

Please do not send private emails asking for help. I've said this dozens of times; it is much more beneficial to the community as a whole to post the gmx-users list, where discussions are archived for future use. You also have a better chance of reaching someone who knows how to solve your p

[gmx-users] Re: water simulation

You shouldn't have [atomtypes] where you declared it below. > Message: 2 > Date: Tue, 25 Aug 2009 16:35:49 +0530 > From: abhijit kayal > Subject: [gmx-users] water simulation > To: gmx-users@gromacs.org > Message-ID: >         > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > With my gr

Re: [gmx-users] Normal mode analysis

abhijit kayal wrote: Hi, If I going to perform normal mode analysis of a protien molecule what are the changes have to be done in .mdp files That's what the manual is for, as well as pertinent literature and textbooks describing the protocols. -Justin Abhijit Kayal

Re: [gmx-users] water simulation

abhijit kayal wrote: --- Program grompp, VERSION 4.0.4 Source code file: topio.c, line: 415 Fatal error: Syntax error - File topol.top, line 4 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes --

[gmx-users] Normal mode analysis

Hi, If I going to perform normal mode analysis of a protien molecule what are the changes have to be done in .mdp files Abhijit Kayal IIT Delhi __

[gmx-users] water simulation

Hi, With my grompp.mdp,topol.top and gonf.gro i gave the command and the output was [abhi...@scfbioserver gromacs]$ grompp -f grompp.mdp -p topol.top -c conf.gro -o water.tpr :-) G R O M A C S (-: Gravel Rubs Often Many Awfully Cauterized Sores

Re: [gmx-users] water simulation

abhijit kayal wrote: Hi everyone, I am new to the GROMACS.In GROMACS there is a example of water(spc model).But after the command grompp -the output file water.tpr should generate.But it is not giving the output.So what kind of changes have to be done in grompp.mdp,topol.top,

[gmx-users] water simulation

Hi everyone, I am new to the GROMACS.In GROMACS there is a example of water(spc model).But after the command grompp -the output file water.tpr should generate.But it is not giving the output.So what kind of changes have to be done in grompp.mdp,topol.top, files.Please reply.