[gmx-users] xpm2ps

Hello everyone When I use xpm2ps in Gromacs 2018.3 and open .eps file, I see that a balck line cover the numbers in y and x axis. Any person can help me?! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Add residue to force field

Hello. For my MD I need a GTP residue. So I made it by modifying ATP residue in gromos 54A7 force field by guanosine base. First time I save it in GTP.rtp and my energy minimisation steps was 30,000 steps because of one atom in GTP. In next try I add GTP residue in aminoaciduria.rtp which contains

Re: [gmx-users] Topology file

thanks Justin for your helps. the pdb2gmx make posre_chain_A.itp but don't write any thing about it in my topol.top!!! Can I add it in my topol.top file?! And what's its template for it?! On Fri, 5 Oct 2018 17:08 Justin Lemkul, wrote: > > > On 10/4/18 6:53 PM, Mahdi Sobati Nez

Re: [gmx-users] Topology file

ce. Hope it helps! > > Best > > Rose > > > > On Wed, 10 Oct 2018, 16:21 Mahdi Sobati Nezhad, < > mahdisobatinez...@gmail.com> > wrote: > > > Thanks rose. Can you tell me more about which cases I should use position > > restrictions?! > > Thanks >

Re: [gmx-users] Topology file

t; But whenever you use define=-DPOSRES in your .mdp file, GROMACS can read > posre.itp files in topol.top an apply position restriction to molecule. > > Rose > > On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, < > mahdisobatinez...@gmail.com> > wrote: > > > Hell

[gmx-users] Topology file

Hello Gromacs users. When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there is no any porse.itp What can I do?! Do it's important that porse.itp should be in topol.top or its enough that pdb2gmx make porse.itp?! Thanks -- Gromacs Users mailing list * Please search the archive

[gmx-users] Change in atom name

Hello Gromacs users. My ligand have two 'Cl' atoms. I cut atoms from ligand.gro and paste it in complex.gro and then open complex.gro in VMD and I see that the VMD shows my atoms as Carbon!!! Do this will not have any effect in my MD?! Thanks -- Gromacs Users mailing list * Please search the

[gmx-users] Topology file.

Hello everyone I use Gromacs 18.3. when I use the command "gmx pdb2gmx -f protein.pdb -o protein.gro" it makes a topology file. But this topology haven't "posre_Chain _A.itp" or any other posre in part "; Include chain topologies" im confused, that what is wrong?! Do I can add this posre parts

Re: [gmx-users] HB3 ATOM

please excuse me sir On Mon, 3 Sep 2018 22:59 Justin Lemkul, wrote: > > > On 9/3/18 2:28 PM, Mahdi Sobati Nezhad wrote: > > how can I build hydrogens own, after -ignh command?! > > Please re-read what I just said. > > -Justin > > > On Mon, 3

Re: [gmx-users] HB3 ATOM

how can I build hydrogens own, after -ignh command?! On Mon, 3 Sep 2018 22:55 Justin Lemkul, wrote: > > > On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote: > > Yes. Now my problem is HG in residue CYS that I don't know rename to > what!!! > > Either the names in the

Re: [gmx-users] HB3 ATOM

Yes. Now my problem is HG in residue CYS that I don't know rename to what!!! On Mon, 3 Sep 2018 22:49 Justin Lemkul, wrote: > > > On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote: > > Hi > > my pdb file named HB2 and HB3 but .rtp file in my force field named > HB1and > &

[gmx-users] HB3 ATOM

Hi my pdb file named HB2 and HB3 but .rtp file in my force field named HB1and HB2. and so on error "atom HB3 in residue xxx was not found in rtp entry" can I rename HB2 to HB1 and HB3 to HB2 ? or any idea?! -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Getting ligand's topology

can I use SWISSPARAM or MATCH servers?! On Wed, 22 Aug 2018 23:50 Justin Lemkul, wrote: > > > On 8/22/18 3:18 PM, Mahdi Sobati Nezhad wrote: > > Thanks, do acpype is for charmm?! > > > No, it is for AMBER. > > -Justin > > > On Wed, 22 Aug 201

Re: [gmx-users] Getting ligand's topology

gt; > > > > On 8/20/18 2:40 AM, Mahdi Sobati Nezhad wrote: > > > >> thanks for your taking time. and so on for a begginer like me there is > no > >> any way > >> > > > > Well, there is if you're willing to invest the time in learning some

Re: [gmx-users] Getting ligand's topology

on and refinement is > still an advanced concept that is best suited for experienced users, as > knowledge of fundamental principles of MD, QM, and empirical energy > functions is required. > > -Justin > > > Thank you > > > > > > On Sun, 19 Aug 2018 at 1:3

Re: [gmx-users] Getting ligand's topology

big which will > be time consuming. Or you have to adapt divide and conquer method, which is > going to be complicated. So it’s your wise choice always. Maybe others, > especially Dr. Justin or Dr. Mark could give you a better soln. > > Thank you > > On Sat, 18 Aug 2018 at

Re: [gmx-users] Getting ligand's topology

sonally don’t appreciate this method as it is very time consuming if > your structure is big and having penalties in dihedrals which again make it > complicated. > Thank you > > On Sat, 18 Aug 2018 at 7:02 PM, Mahdi Sobati Nezhad < > mahdisobatinez...@gmail.com> wrote: > > &g

[gmx-users] Getting ligand's topology

Hi I'm a begginer in taking ligand's topology from CGENFF and my '.str' file have some high penalty numbers. What I can do?! And how I can do validation and optimization?! I read the FAQ in its server but I don't understand!!! Thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] GTP

AM, Mahdi Sobati Nezhad wrote: > > hello > > I'm working on a protein that contains GTP in its structure. I can't find > > any force field that contains GTP's residue but I find a force field that > > contains the ATPs residue! There is any way that I can convert ATP to > GT

[gmx-users] GTP

hello I'm working on a protein that contains GTP in its structure. I can't find any force field that contains GTP's residue but I find a force field that contains the ATPs residue! There is any way that I can convert ATP to GTP?! Or any other idea?! (I work with gromos 43a1 force field) thanks --