[gmx-users] No default U-B types in CHARMM36 FF
Justin Lemkul
jalemkul at vt.edu
Sun Apr 13 15:51:31 CEST 2014
On 4/13/14, 6:39 AM, Mark Abraham wrote:
> Hi,
>
> Looks like nobody has parametrized that interaction. Not too surprising,
> though, since you won't often get NH2 in water at biological pH!
>
Yep, just another obscure case that was never deemed important enough to
parametrize. Assigning parameters by analogy here is probably safe enough, e.g.
the H-NH2-CT1 parameters can be used for H-NH2-CT2.
-Justin
> Mark
> On Apr 13, 2014 10:16 AM, "Albert" <mailmd2011 at gmail.com> wrote:
>
>> Hello:
>>
>> I am running command:
>>
>> grompp -f em.mdp -c ion-em.pdb -o test.tpr
>>
>>
>> but it failed with messages:
>>
>>
>>
>> ------------------------------------------------------------
>> -----------------------------------------
>>
>> Generated 71611 of the 71631 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 45719 of the 71631 1-4 parameter combinations
>>
>> ERROR 1 [file topol.top, line 22781]:
>> No default U-B types
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.6.5
>> Source code file: /home/albert/gromacs-4.6.5/src/kernel/grompp.c, line:
>> 1610
>>
>> Fatal error:
>> There were 13 errors in input file(s)
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>>
>>
>> I checked the line 22781, it was the last line of following:
>>
>> [ angles ]
>> ; ai aj ak funct c0 c1 c2 c3
>> 2 1 3 5
>> 2 1 4 5 (<---this line)
>>
>>
>>
>> Here is my initial residues:
>>
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass typeB
>> chargeB massB
>> ; residue 36 GLY rtp GLY q 0.0
>> 1 NH2 36 GLY N 1 -0.96 14.007 ; qtot
>> -0.96
>> 2 H 36 GLY HT1 2 0.34 1.008 ; qtot
>> -0.62
>> 3 H 36 GLY HT2 3 0.34 1.008 ; qtot
>> -0.28
>> 4 CT2 36 GLY CA 4 0.1 12.011 ; qtot
>> -0.18
>> 5 HB2 36 GLY HA1 5 0.09 1.008 ; qtot
>> -0.09
>> 6 HB2 36 GLY HA2 6 0.09 1.008 ; qtot 0
>> 7 C 36 GLY C 7 0.51 12.011 ; qtot
>> 0.51
>> 8 O 36 GLY O 8 -0.51 15.999 ; qtot 0
>> ; residue 37 SER rtp SER q 0.0
>> 9 NH1 37 SER N 9 -0.47 14.007 ; qtot
>> -0.47
>> 10 H 37 SER HN 10 0.31 1.008 ; qtot
>> -0.16
>> 11 CT1 37 SER CA 11 0.07 12.011 ; qtot
>> -0.09
>> 12 HB1 37 SER HA 12 0.09 1.008 ; qtot 0
>> 13 CT2 37 SER CB 13 0.05 12.011 ; qtot
>> 0.05
>> 14 HA2 37 SER HB1 14 0.09 1.008 ; qtot
>> 0.14
>> 15 HA2 37 SER HB2 15 0.09 1.008 ; qtot
>> 0.23
>> 16 OH1 37 SER OG 16 -0.66 15.999 ; qtot
>> -0.43
>> 17 H 37 SER HG1 17 0.43 1.008 ; qtot 0
>> 18 C 37 SER C 18 0.51 12.011 ; qtot
>> 0.51
>> 19 O 37 SER O 19 -0.51 15.999 ; qtot 0
>> ; residue 38 PRO rtp PRO q 0.0
>> 20 N 38 PRO N 20 -0.29 14.007 ; qtot
>> -0.29
>> 21 CP3 38 PRO CD 21 0 12.011 ; qtot
>> -0.29
>> 22 HA2 38 PRO HD1 22 0.09 1.008 ; qtot
>> -0.2
>> 23 HA2 38 PRO HD2 23 0.09 1.008 ; qtot
>> -0.11
>> 24 CP1 38 PRO CA 24 0.02 12.011 ; qtot
>> -0.09
>> 25 HB1 38 PRO HA 25 0.09 1.008 ; qtot 0
>> 26 CP2 38 PRO CB 26 -0.18 12.011 ; qtot
>> -0.18
>> 27 HA2 38 PRO HB1 27 0.09 1.008 ; qtot
>> -0.09
>> 28 HA2 38 PRO HB2 28 0.09 1.008 ; qtot 0
>> 29 CP2 38 PRO CG 29 -0.18 12.011 ; qtot
>> -0.18
>> 30 HA2 38 PRO HG1 30 0.09 1.008 ; qtot
>> -0.09
>> 31 HA2 38 PRO HG2 31 0.09 1.008 ; qtot 0
>> 32 C 38 PRO C 32 0.51 12.011 ; qtot
>> 0.51
>> 33 O 38 PRO O 33 -0.51 15.999 ; qtot 0
>> ; residue 39 GLY rtp GLY q 0.0
>> 34 NH1 39 GLY N 34 -0.47 14.007 ; qtot
>> -0.47
>> 35 H 39 GLY HN 35 0.31 1.008 ; qtot
>> -0.16
>> 36 CT2 39 GLY CA 36 -0.02 12.011 ; qtot
>> -0.18
>> 37 HB2 39 GLY HA1 37 0.09 1.008 ; qtot
>> -0.09
>> 38 HB2 39 GLY HA2 38 0.09 1.008 ; qtot 0
>> 39 C 39 GLY C 39 0.51 12.011 ; qtot
>> 0.51
>> 40 O 39 GLY O 40 -0.51 15.999 ; qtot 0
>>
>>
>> I used command:
>>
>> pdb2gmx -f p.pdb -o gmx.pdb -ter
>>
>> to generate the topology file, and I assinged: GLY-NH2 for the first
>> residue GLY, -COOH for the last residue.
>>
>> thank you very much.
>>
>> best
>> Albert
>>
>>
>>
>>
>>
>>
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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 601
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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