[gmx-users] gmx select

[Pandya, Akash]

So I tried with both opening and closing. It seems to select all the molecules in my box which is not what I want. I only want certain glycine molecules that are closest to the protein. May you please suggest another way is which I could achieve this. The command I used is below:

gmx select -f output.xtc -s output.gro -select '"Close to protein" resname Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb 

Akash


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: 13 July 2017 14:01
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gmx select



On 7/13/17 3:38 AM, Pandya, Akash wrote:
> gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"'
> 

I suspect Mark is right, this is an invalid command, because you have a closing ' without an opening ' in your -select argument.  This should fail with a generic error message that the selection can't be parsed.  I am also curious about "resname Glyci" because if that's the case, then you must have hacked some force field files, because everyone calls glycine "GLY" per standard nomenclature.

-Justin

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se 
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf 
> Of Mark Abraham
> Sent: 13 July 2017 00:04
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx select
> 
> Hi,
> 
> Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes.
> 
> Mark
> 
> On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:
> 
>> I have used the same name in my coordinate file. For Glycine it is 
>> spelt as Glyci, so the word has been cut off. I know this is correct 
>> because I use the same name in VMD.
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark 
>> Abraham
>> Sent: 12 July 2017 22:42
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] gmx select
>>
>> Hi,
>>
>> What are the residue names in your coordinate file? Glyci probably 
>> doesn't fit
>>
>> Mark
>>
>> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
>> <akash.pandya.15 at ucl.ac.uk>
>> wrote:
>>
>>> Hi all,
>>>
>>>
>>> I am trying to select all the glycine molecules with 0.5nm of my protein.
>>> I tried both of these commands I got from the gromacs website:
>>>
>>> gmx select -f output.gro -select "Close to protein" resname Glyci 
>>> and within 0.5 of group "Protein"' -ofpdb
>>>
>>> gmx select -f output.xtc -s output.tpr (my converted input file) 
>>> -select "Close to protein" resname Glyci and within 0.5 of group 
>>> "Protein"' -ofpdb
>>>
>>>
>>> Nothing comes up when I enter them. Please could someone help me 
>>> with
>> this?
>>>
>>>
>>> Akash
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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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