[gmx-users] Get a correct .pdb for a synthetic peptide

[Tomasz Piskorz]

Hi,

I quite often use Avogadro and it always works. Just, remember to change
names of the residues/molecules in pdb that they match with topology file.

Cheers,
Tomasz

On 8 March 2017 at 10:36, Sotirios Dionysios I. Papadatos <
si.papadatos at edu.cut.ac.cy> wrote:

> Hi, to get things straight did you use pdb2gmx or just editconf? Where
> does the error occur?
>
> My personal choice is Maestro which is free for academic use. The
> resulting pdbs' have no problem with Gromacs.
>
> If you want to make minor changes, for example change LIG to DRG (assuming
> DRG is mentioned in the ff) then yes you can use a text editor.
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of FL S <
> frank.leonard.schmidt at gmail.com>
> Sent: Wednesday, March 8, 2017 11:01:13 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Get a correct .pdb for a synthetic peptide
>
> Hello,
>
>
> I want to run a gromacs MD for a small synthesized peptide. All used amino
> acids are known for and defined in gromacs, as are the termini.
> Consequently it would be ideal to use pdb2gmx to create the*.gro, *.top and
> *.itp, but I have troubles creating a syntactically correct *.pdb input
> file.
>
>
> I created  *.pdb (or *.mol2) files using standard chemistry software such
> as Chem3D and Avogadro, and also tried VMD and PRODMG, but never get a
> *.pdb file readable by gromacs. Using editconf leads to a fatal error as
> all atoms are assigned to residue DRG which is not defined. Using
> swissparam for gives the same problem, just that now it is LIG, not DRG.
> (and I ideally want to work with OPLS, not CHARMM). The only option I see
> is to use an editor to manually change the atom numbering and to group the
> atoms into amino acids, but this seems very tedious.
>
>
> What is the usual “pipeline” you are using in order to create your own
> molecular structure and import them into gromacs? Is there a tutorial?
>
>
> I am working with gromacs 5.1.4 in a linux environment and am able to do
> simulations using *.pdb input files downloaded from rcsb.org.
>
>
> Thanks in advance
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