[gmx-users] pdb2gmx disulfide bond in dimer

[Justin Lemkul]

On 4/14/16 6:32 AM, s.varriale wrote:
>
> Dear all,
> I try to perform a MD simulation of a covalent dimer with gromacs 4.5.4.
> I do:
> pdb2gmx -f prot.pdb -chainsep ter
> and the programme generates a .gro file with disulfide bond.
> but when i want to minimize the system, there is an error:
>
> There were 2 inconsistent shifts. Check your topology
> Warning: 1-4 interaction between 45 and 387 at distance 8.995 which is larger
> than the 1-4 table size 2.200 nm
>
> if I try to simulate the 2 chains separatly, there is any error.
> What can i do?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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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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