[gmx-users] pdb2gmx disulfide bond in dimer

[Justin Lemkul]

On 4/14/16 9:53 AM, s.varriale wrote:
> 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.
>

As it should.  The two chains have to be merged into a single [moleculetype] 
definition for that bond to be created.  The merging process isn't causing 
stability; some other aspect of your structure is.  The link I provided includes 
all the usual diagnostic information.  Unless you go through those steps (and 
have a look through some of the other million or so posts regarding the same 
issue) and provide some more useful details about what you observe, there's 
little anyone else can suggest.

-Justin

> Sonia
> 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 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
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>

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

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

==================================================