[gmx-users] Simulating Multiple Solute Particles
Nathan K Houtz
nhoutz at purdue.edu
Tue Nov 4 06:58:38 CET 2014
Thanks for your reply. However, I'm still confused. I thought that the command:
#include "oplsaa.ff/tip3p.itp"
is a call to the opls-aa force field. If this is not the correct way to include the force field parameters, how should I do that?
Regards,
Nathan Houtz
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Monday, November 3, 2014 12:44:52 PM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles
On 11/3/14 12:50 AM, Nathan K Houtz wrote:
> Sorry everybody, I accidentally unsubscribed from the mailing list and missed my last response. Dr. Lemkul posted a message but I can't reply directly to it, so here's what he said:
>
>> Your topology is constructed incorrectly, but without seeing it in its entirety, it is impossible to say. Please post the file for download somewhere and provide a link, otherwise copy and paste its entire contents into a reply if the message will be small enough.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
>> jalem... at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>
> Thank you Justin! I think it's easier to just paste it here. This is my topol.top file:
>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 2 yes 0.5 0.5
>>
>> [ atomtypes ]
>> ;name at.num mass charge ptype sigma epsilon
>> CH3 15 15.03500 0.000 A 0.39100 0.66944 ;united atom Methyl [C-CH3]
>> C 12 12.01100 0.000 A 0.35000 0.27614 ;C [R3CCOO-] (first carbon)
>> CM 12 12.01100 0.000 A 0.37500 0.43932 ;carboxyl C [R-(C=O)-OH]
>> O 8 15.99940 0.000 A 0.30800 0.71128 ;carboxyl O [C-O-H]
>> OM 8 15.99940 0.000 A 0.29600 0.87864 ;carbonyl O [C=O]
>> H 1 1.00794 0.000 A 0.00000 0.00000 ;carboxyl H [C-O-H]
>> OW 8 15.99940 0.000 A 0.31660 0.65000
>> HW 1 1.00794 0.000 A 0.00000 0.00000
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> TETR 3
>>
>> [ atoms ]
>> ; nr type resnr residu atom cgnr charge mass
>> 1 CH3 1 TETR C1 1 0 15.03500
>> 2 C 1 TETR C2 1 0 12.01100
>> 3 C 1 TETR C3 1 0 12.01100
>> 4 CM 1 TETR C4 1 0.38 12.01100
>> 5 OM 1 TETR O1 1 -0.38 15.99940
>> 6 O 1 TETR O2 1 -0.40 15.99940
>> 7 H 1 TETR H4 1 0.40 1.00794
>>
>> [constraints]
>> ; i j funct distance
>> 1 2 1 0.14550
>> 2 3 1 0.11780
>> 3 4 1 0.14420
>> 4 5 1 0.12040
>> 4 6 1 0.13100
>> 6 7 1 0.89000
>>
>> ; Include SPC water topology
>> #include "oplsaa.ff/tip3p.itp"
>>
Here's your problem. Look at the contents of tip3p.itp:
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_111 1 SOL OW 1 -0.834
2 opls_112 1 SOL HW1 1 0.417
3 opls_112 1 SOL HW2 1 0.417
It uses OPLS-AA atom types, but you haven't defined what those are because
nothing above calls the OPLS-AA force field. Hence, grompp dies because it does
not know how to assign nonbonded parameters to opls_111 or opls_112.
>> [ system ]
>> Tetrolic Acid in water
>>
>> [ molecules ]
>> Tetrolic Acid 500
>> SOL 5481
>
> I made the file myself, so I hope I didn't make any syntax errors. I discovered with the .gro file that the spacing is very important since gromacs doesn't use delimiters but allows only a fixed number of characters for each entry. Is the .top file the same way? I just used a template from some example file and tried to make the numbers fit appropriately under the headings. If it's not correct, why didn't gromacs complain when I solvated it? Doesn't it read in the topology file then as well?
>
Topologies do not have the same formatting requirements.
-Justin
--
==================================================
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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