[gmx-users] More dihedrals generated than provided in the, force field & "No default Proper Dih. types" as a result
tyugashev at niboch.nsc.ru
Thu Dec 28 07:19:26 CET 2017
28.12.2017 02:39, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> Message: 3
> Date: Wed, 27 Dec 2017 13:46:37 -0500
> From: Justin Lemkul<jalemkul at vt.edu>
> To:gmx-users at gromacs.org
> Subject: Re: [gmx-users] More dihedrals generated than provided in the
> force field & "No default Proper Dih. types" as a result
> Message-ID:<c76426b1-eb96-3043-dfe9-5ff6fb8004f7 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> On 12/27/17 9:39 AM, Timofey Tyugashev wrote:
>> I'm building a protein with a cubic [Fe4S4] cluster using parameters
>> from a published paper.
>> This parameters provide only two dihedral angles types (S-FE-SG-CB and
>> FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong
>> to the Cys residue).
>> GROMACS automatically generates far more dihedrals with types like
>> S-FE-S-FE (looks like all of them are inta-cluster) which are omitted
>> in the source paper and are explicitly stated to be redundant for MD.
>> However? grommp generates errors and stops:
>> ERROR 49 [file topol.top, line 32916]:
>> ? No default Proper Dih. types
>> How to solve this problem?
> pdb2gmx automatically generates all possible dihedrals. If they are not
> necessary in your force field description, either remove the offending
> lines from your topology or assign them dihedral parameters with force
> constants equal to zero so they impose no force.
Yes, right after sending the message I realised that the redundant
dihedrals could be simply removed from the .top file. Seems to be
running fine now.
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