[gmx-users] Regarding coordinate mismatching.

[Justin Lemkul]

On 8/27/13 5:59 AM, sanjay choubey wrote:
> Hi,
>   I am running membrane dynamics. After giving this commnad
>
>
>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>
>    i am receiving the following errors:
> Generated 837 of the 2346 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'NA'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: grompp.c, line: 523
>
> Fatal error:
> number of coordinates in coordinate file (em.gro, 44494)
>               does not match topology (topol.top, 43374)
>   ------------------------------------------------------------
>
>                                                     I am not getting how to rectify the error, number of coordinates in coordinate file em.gro(44494) doesnot
>   match topology(topol.top, 43374).
>

The answer is always bookkeeping.  You haven't correctly accounted for some part 
of the system in the [molecules] directive.  The difference is 1120, so it's not 
related to water molecules.  You also say you're running a membrane system, but 
I see no evidence of lipids in the grompp output, but if indeed there are 
lipids, you likely had to remove some to accommodate the protein, but didn't 
remove them from the topology.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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