[gmx-users] pdb2gmx disulfide bond in dimer
s.varriale at ibp.cnr.it
Thu Apr 14 15:52:02 CEST 2016
thank you Justin, but I can't understand how to solve my problem.
when pdb2gmx links the 2 CYS, the resulting .gro file shows a unique
chain because N- and C- termini of 2 chains are linked.
Il 14/04/2016 13:46 Justin Lemkul ha scritto:
> 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
>> 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
>> 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?
> 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
Sonia Varriale, PhD
More information about the gromacs.org_gmx-users