[gmx-users] Protein-Ligand complex Implicit simulation

[Justin Lemkul]

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On 5/20/15 9:54 AM, sunita gupta wrote:
> Thanks Justin for your reply
>
> Below is the  file where I added h1 parameters in gbsa.itp...In the same
> way I added the parameters for all the possible atomtypes from gaff ff
>
> [ implicit_genborn_params ]
>
> ; atype      sar      st     pi       gbr       hct
> ;Br           0.1      1      1        0.125     0.85 ; H
> C            0.172    1      1.554    0.1875    0.72 ; C
> CA           0.18     1      1.037    0.1875    0.72 ; C
> CB           0.172    0.012  1.554    0.1875    0.72 ; C
> CC           0.172    1      1.554    0.1875    0.72 ; C
> CN           0.172    0.012  1.554    0.1875    0.72 ; C
> CR           0.18     1      1.073    0.1875    0.72 ; C
> CT           0.18     1      1.276    0.190     0.72 ; C
> CV           0.18     1      1.073    0.1875    0.72 ; C
> CW           0.18     1      1.073    0.1875    0.72 ; C
> C*           0.172    0.012  1.554    0.1875    0.72 ; C
> H            0.1      1      1        0.115     0.85 ; H
> HC           0.1      1      1        0.125     0.85 ; H
> H1           0.1      1      1        0.125     0.85 ; H
> HA           0.1      1      1        0.125     0.85 ; H
> H4           0.1      1      1        0.115     0.85 ; H
> H5           0.1      1      1        0.125     0.85 ; H
> HO           0.1      1      1        0.105     0.85 ; H
> HS           0.1      1      1        0.125     0.85 ; H
> HP           0.1      1      1        0.125     0.85 ; H
> N            0.155    1      1.028    0.17063   0.79 ; N
> NA           0.155    1      1.028    0.17063   0.79 ; N
> NB           0.155    1      1.215    0.17063   0.79 ; N
> N2           0.16     1      1.215    0.17063   0.79 ; N
> N3           0.16     1      1.215    0.1625    0.79 ; N
> O            0.15     1      0.926    0.148     0.85 ; O
> OH           0.152    1      1.080    0.1535    0.85 ; O
> O2           0.17     1      0.922    0.148     0.85 ; O
> S            0.18     1      1.121    0.1775    0.96 ; S
> SH           0.18     1      1.121    0.1775    0.96 ; S
>
>
> *h1           0.1      1      1        0.139     0.85 ; H *
> The error is "Couldn't find topology match for atomtype h1
> Aborted (core dumped)"
>

A quick look through the code suggests that when grompp parses the gbsa.itp file 
and finds "h1" it cannot find that atom type in the force field, so something 
outside of the gbsa.itp file itself is the problem, e.g. you're providing a type 
that doesn't exist or otherwise isn't used.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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