[gmx-users] GRO File Merging

[Justin Lemkul]

On 2/26/17 10:54 AM, Justin Lemkul wrote:
>
>
> On 2/25/17 3:10 PM, Sanim Rahman wrote:
>> Hello Mark,
>>
>> I was able to get around the issue so no worries. The reason why I split
>> them up because I wanted to describe my lipids in CHARMM36 parameters and
>> protein in CHARMM27 in order to replicate a simulation.
>>
>
> Nitpick: there's no such thing as a CHARMM27 protein force field.  What you're
> using is CHARMM22/CMAP with various revisions that were made to it prior to
> CHARMM36 in 2012.  CHARMM27 refers exclusively to the CHARMM nucleic acid force
> field released in 2000 (which was superseded by the CHARMM36 nucleic acid force

...and the C27 lipids that were included in the force field, of course.  But 
there's no "CHARMM27 protein force field," though you often see that misnomer in 
the literature.

-Justin

> field in 2011, and is much better).
>
> -Justin
>
>> However, is my thought process for the topology file correct?
>>
>> Regards,
>>
>> *Sanim Rahman*
>> B.S. Chemical Engineering, 2019
>> Resident Assistant, Castor Hall Engineering Living Learning Community
>> 2016-2017
>> Co-Founder and Co-President of the Undergraduate Research Society
>> Undergraduate Researcher, Global Center for Hearing and Speech Research
>> <https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
>>
>>
>> On Sat, Feb 25, 2017 at 2:59 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Why are you splitting things up? The whole coordinate file from charmm gui
>>> is the useful thing.
>>>
>>> Mark
>>>
>>> On Sat, 25 Feb 2017 20:21 Sanim Rahman <sanimr at mail.usf.edu> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have been using gromacs to design a membrane protein system. I used
>>>> CHARMM-GUI to design my membrane and then was able to split my system
>>> into
>>>> three parts (protein, lipid, solvent) and convert it into .gro format. I
>>> am
>>>> able to individually view each part in VMD all together but when I use:
>>>>
>>>> *cat protein.gro lipid.gro solvent.gro > system.gro*
>>>>
>>>> The molecule does not show up in VMD. I properly edit the number of atoms
>>>> and the box coordinates of the system by using -editconf to correct the
>>> box
>>>> coordinates. I receive no errors in VMD as well. What should I do to fix
>>>> this?
>>>>
>>>> Also when combining topology files, I would convert lipid.top and
>>>> solvent.top into .itp files and use the #include statement to combine
>>> them
>>>> into my protein.top file? After that, my system should be set correct?
>>>>
>>>> Thank You,
>>>> Sanim Rahman
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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

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