[gmx-users] number of coordinates does not match after POSRES

[Justin Lemkul]

On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote:
> Hi Mark,
> 
> Thanks for your prompt reply. What surprises me is that a change of "define
> = POSRES" could cause a problem. The full output from grompp is -
> 
> checking input for internal consistency...
> calling cpp...
> cpp: error: POSRES: No such file or directory

Well, here's the first problem.  Your syntax is incorrect (#ifdef keywords are 
prefixed with -D, so "define = POSRES" does nothing but "define = -DPOSRES" 
would invoke position restraints.

> cpp: warning: ‘-x c’ after last input file has no effect
> cpp: fatal error: no input files
> compilation terminated.
> cpp exit code: 1024
> Tried to execute: 'cpp  -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top
> POSRES p1p2.top > gromppDTyNuM'
> The 'cpp' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1

Is there a reason you are using prehistoric, deprecated software?

> Source code file: grompp.c, line: 448
> 
> Fatal error:
> number of coordinates in coordinate file (npt.gro, 74787)
>               does not match topology (p1p2.top, 0)
> 

This suggests mangled syntax, so check for typos, bad line endings, etc. and use 
a more modern GROMACS version.

-Justin

> 
> The additional information is attached here as a reference.
> 
> *chainA-pace.top*
> [ moleculetype ]
> ; Name            nrexcl
> Protein_A           3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
>     chargeB      massB
>       1         N+      1    MET      N      1        0.7         17   ;
> qtot 0.7
> .
> .
> .
>    919   922   921   920     2    0.0  300.0
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "chainA_posre.itp"
> #endif
> 
> 
> *chainA_porse.itp*
> ; position restraints for r_1-62_&_Backbone of FullP1P2 in water
> 
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> .
> .
> .
>   523    1       1000       1000       1000
>   530    1       1000       1000       1000
> 
> Simon
> 
> 
> 2017-06-07 16:28 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:
> 
>> Hi,
>>
>> We can't tell, because position restraints are an attribute of
>> moleculetypes and those are hidden in your itp files and you didn't share
>> which moleculetype grompp reported was the problem. Please copy and paste
>> terminal output to make a useful description.
>>
>> You'll need to include the position restraint file appropriate to each
>> moleculetype, of course - not the same one each time.
>>
>> Mark
>>
>> On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu <simoncks1994 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Initially, my topology file can run grompp with .mdp and .gro. However,
>>> after putting POSRES in my mdp, the warning "number of coordinates does
>> not
>>> match" and there is no coordinate recognized in my topology file anymore.
>>> Therefore, the option POSRES somehow changes everything.
>>>
>>> The topology file is put here. Is there anything I have written
>>> incorrectly?
>>>
>>> ; Include forcefield parameters
>>> #include "ffPACE_1.3.itp"
>>>
>>> ; Include chain topologies
>>> #include "chainA-pace.top"
>>> #include "chainB-pace.top"
>>>
>>> ; Include water topology
>>> #include "cgWater.itp"
>>>
>>> ; Include topology for ions
>>> #include "martini_v2.0_ions.itp"
>>>
>>> [ system ]
>>> ; Name
>>> FullP1P2 in water
>>>
>>> [ molecules ]
>>> ; Compound        #mols
>>> Protein_A     1
>>> Protein_B     1`
>>> SOL             72899
>>> NA+             20
>>> --
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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

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