[gmx-users] converting pdb file to gromacs input file
Mark Abraham
mark.j.abraham at gmail.com
Sat Jan 14 19:28:17 CET 2017
Hi,
You are trying to generate a topology, but pdb2gmx can only do that if it
recognizes the molecule already, If you want generate a topology for an
arbitrary molecule, then you should look at various online servers, like
ATB, SwissParam and others.
If you've done all the available online tutorial material, then you'll be
much better placed to do this.
Mark
On Sat, Jan 14, 2017 at 12:02 PM Subashini .K <subashinik at hotmail.com>
wrote:
>
>
> It says, RESIDUE NOT FOUND in residue topology database
>
>
> For example in methane, the example was
>
>
>
> COMPND METHANE
> AUTHOR GENERATED BY OPEN BABEL 2.3.2
> HETATM 1 C CH4 1 -0.370 0.900 0.000 1.00 0.00
> C
> HETATM 2 H1 CH4 1 0.700 0.900 0.000 1.00 0.00
> H
> HETATM 3 H2 CH4 1 -0.727 0.122 0.643 1.00 0.00
> H
> HETATM 4 H3 CH4 1 -0.727 0.731 -0.995 1.00 0.00
> H
> HETATM 5 H4 CH4 1 -0.727 1.845 0.351 1.00 0.00
> H
> END
>
>
> What does CH4 mean here?
>
>
> Then, should we mention the hybridization of each and every atom?
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sotirios
> Dionysios I. Papadatos <si.papadatos at edu.cut.ac.cy>
> Sent: Saturday, January 14, 2017 4:06 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] converting pdb file to gromacs input file
>
> In pdb2gmx you give as an input the filename.pdb. This should do the
> trick. But I think there is something else that you truly need. Maybe you
> need some more info on how to add a hetatm in an existing force field.?
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Subashini
> .K <subashinik at hotmail.com>
> Sent: Saturday, January 14, 2017 12:04:40 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] converting pdb file to gromacs input file
>
> Hi gromacs users,
>
>
> I am a new gromacs user.
>
>
> I wanted to generate a .gro, .itp, .conf file using the command
>
>
> $ gmx pdb2gmx -f lig.pdb
>
>
> However, the pdb file must be in the required format.
>
> What should we type instead of LIG corresponding to each and every atom?
>
>
> This is an example file of phenylcyclohexane.
>
> Please tell me how to proceed further?
>
>
> COMPND Phenylcyclohexane
> AUTHOR GENERATED BY OPEN BABEL 2.3.2
> HETATM 1 C LIG 1 -2.801 1.177 0.180 1.00 0.00
> C
> HETATM 2 C LIG 1 -1.406 1.177 0.180 1.00 0.00
> C
> HETATM 3 C LIG 1 -0.708 2.371 0.000 1.00 0.00
> C
> HETATM 4 C LIG 1 -1.405 3.566 -0.181 1.00 0.00
> C
> HETATM 5 C LIG 1 -2.800 3.566 -0.181 1.00 0.00
> C
> HETATM 6 C LIG 1 -3.498 2.372 -0.001 1.00 0.00
> C
> HETATM 7 H LIG 1 -3.350 0.236 0.322 1.00 0.00
> H
> HETATM 8 H LIG 1 -0.856 0.235 0.323 1.00 0.00
> H
> HETATM 9 H LIG 1 -0.855 4.508 -0.323 1.00 0.00
> H
> HETATM 10 H LIG 1 -3.350 4.508 -0.324 1.00 0.00
> H
> HETATM 11 H LIG 1 -4.598 2.372 -0.001 1.00 0.00
> H
> HETATM 12 C LIG 1 0.832 2.372 0.001 1.00 0.00
> C
> HETATM 13 C LIG 1 1.339 1.686 1.253 1.00 0.00
> C
> HETATM 14 C LIG 1 1.341 1.681 -1.248 1.00 0.00
> C
> HETATM 15 H LIG 1 1.170 3.441 -0.001 1.00 0.00
> H
> HETATM 16 C LIG 1 2.852 1.589 1.256 1.00 0.00
> C
> HETATM 17 H LIG 1 0.900 0.655 1.317 1.00 0.00
> H
> HETATM 18 H LIG 1 0.998 2.254 2.157 1.00 0.00
> H
> HETATM 19 C LIG 1 2.853 1.585 -1.246 1.00 0.00
> C
> HETATM 20 H LIG 1 0.902 0.650 -1.309 1.00 0.00
> H
> HETATM 21 H LIG 1 1.002 2.245 -2.155 1.00 0.00
> H
> HETATM 22 C LIG 1 3.361 0.900 0.006 1.00 0.00
> C
> HETATM 23 H LIG 1 3.190 1.023 2.162 1.00 0.00
> H
> HETATM 24 H LIG 1 3.291 2.620 1.318 1.00 0.00
> H
> HETATM 25 H LIG 1 3.194 1.016 -2.150 1.00 0.00
> H
> HETATM 26 H LIG 1 3.291 2.615 -1.311 1.00 0.00
> H
> HETATM 27 H LIG 1 4.482 0.903 0.007 1.00 0.00
> H
> HETATM 28 H LIG 1 3.027 -0.170 0.008 1.00 0.00
> H
>
> Thanks,
> Subashini.K
>
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