[gmx-users] Error with moleculetype

[Pandya, Akash]

Tried to put it at the end but it still came up with the same error. 

Justin, I don't understand what you mean?

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: 19 May 2017 22:35
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error with moleculetype



On 5/19/17 5:33 PM, Mark Abraham wrote:
> Hi,
>
> Ok. Maybe it needs to be last in the molecules?
>

Or perhaps the error points to a malformed line ending that causes genion to choke when updating the topology.

-Justin

> Mark
>
> On Fri, 19 May 2017 23:19 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:
>
>> It was the genion command. Here is the message.
>>
>> Fatal error:
>> No line with moleculetype 'SOL' found the [ molecules ] section of 
>> file 'topol.top'
>>
>> -----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: 19 May 2017 21:26
>> To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
>> Subject: Re: [gmx-users] Error with moleculetype
>>
>> Hi,
>>
>> I don't think grompp can issue that message. What was the message you 
>> copied and pasted from your terminal?
>>
>> Mark
>>
>> On Fri, 19 May 2017 18:49 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:
>>
>>> Hi all,
>>>
>>> I have received an error message shown below.
>>>
>>> Fatal error:
>>> No line with moleculetype 'SOL' found the [ molecules ] section of 
>>> file 'topol.top'
>>>
>>> For more information and tips for troubleshooting, please check the 
>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>>
>>> I don't understand what's wrong with my topol.top file. I have 
>>> included the following before the [ molecules ] section.
>>>
>>> [ moleculetype ]
>>> ; Name
>>> SOL                 1
>>>
>>> My [ molecules ] section looks like this:
>>>
>>> [ molecules ]
>>> ; Compound        #mols
>>> Protein_chain_H     1
>>> SOL             73337
>>> Citrate            29
>>> GLY               984
>>>
>>>
>>> I have read the documentation and still don't understand. Please can 
>>> you advise me on what to do?
>>>
>>> Many thanks,
>>> 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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