[gmx-users] adding a new residue into an existing force field?
Justin Lemkul
jalemkul at vt.edu
Fri Dec 5 13:37:34 CET 2014
On 12/5/14 2:59 AM, marzieh dehghan wrote:
> Hi
> according to the previous email, since I want to keep covalent bond during
> the MD using gromacs, you said me, I should add a new residue into an
> existing force field
> <http://www.gromacs.org/Documentation/Terminology/Force_Fields>, but I have
> two questions?
>
> 1- based on the gromacs website , I can copy residuetypes.dat and
> spcbond.dat in the working directory. is it possible to copy
> " amino acid.rtp, aminoacid.hdb, atomtypes.atp" in the working directory?
>
No, you need a full force field directory in the working directory, then make
modifications to the files in it.
> 2- can I use one of the output file of prodrug server (the gromacs
> topology) as aminoacid.rtp?
> (copy at the end of aminoacid.rtp or it use as an independent file?)
>
The format for .itp and .rtp is different; see the manual.
You shouldn't use parameters directly from PRODRG anyway; they're almost always
unreliable.
-Justin
> [ moleculetype ]
> ; Name nrexcl
> GLC 3
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OM 1 UNK OAF 1 -0.322 15.9994
> 2 P 1 UNK PAE 1 1.063 30.9738
> 3 OM 1 UNK OAG 1 -0.322 15.9994
> 4 OM 1 UNK OAH 1 -0.322 15.9994
> 5 OA 1 UNK OAD 1 -0.097 15.9994
> 6 CH2 1 UNK CAC 2 -0.044 14.0270
> 7 C 1 UNK CAB 2 0.184 12.0110
> 8 OA 1 UNK OAA 2 -0.149 15.9994
> 9 H 1 UNK HAA 2 -0.013 1.0080
> 10 C 1 UNK CAI 2 0.184 12.0110
> 11 OA 1 UNK OAJ 2 -0.149 15.9994
> 12 H 1 UNK HAJ 2 -0.013 1.0080
> 13 C 1 UNK CAK 3 0.218 12.0110
> 14 OA 1 UNK OAL 3 -0.126 15.9994
> 15 H 1 UNK HAL 3 -0.011 1.0080
> 16 C 1 UNK CAM 3 0.218 12.0110
> 17 OA 1 UNK OAN 3 -0.126 15.9994
> 18 H 1 UNK HAN 3 -0.011 1.0080
> 19 CH2 1 UNK CAO 3 -0.025 14.0270
> 20 OA 1 UNK OAP 3 -0.126 15.9994
> 21 H 1 UNK HAQ 3 -0.011 1.0080
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 2 1 2 0.148 8600000.0 0.148 8600000.0 ; PAE OAF
> 2 3 2 0.148 8600000.0 0.148 8600000.0 ; PAE OAG
> 2 4 2 0.148 8600000.0 0.148 8600000.0 ; PAE OAH
> 2 5 2 0.161 4840000.0 0.161 4840000.0 ; PAE OAD
> 6 5 2 0.143 8180000.0 0.143 8180000.0 ; CAC OAD
> 7 6 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAC
> 7 8 2 0.136 10200000.0 0.136 10200000.0 ; CAB OAA
> 7 10 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAI
> 8 9 2 0.100 15700000.0 0.100 15700000.0 ; OAA HAA
> 10 11 2 0.136 10200000.0 0.136 10200000.0 ; CAI OAJ
> 10 13 2 0.153 7150000.0 0.153 7150000.0 ; CAI CAK
> 11 12 2 0.100 15700000.0 0.100 15700000.0 ; OAJ HAJ
> 13 14 2 0.136 10200000.0 0.136 10200000.0 ; CAK OAL
> 13 16 2 0.153 7150000.0 0.153 7150000.0 ; CAK CAM
> 14 15 2 0.100 15700000.0 0.100 15700000.0 ; OAL HAL
> 16 17 2 0.136 10200000.0 0.136 10200000.0 ; CAM OAN
> 16 19 2 0.153 7150000.0 0.153 7150000.0 ; CAM CAO
> 17 18 2 0.100 15700000.0 0.100 15700000.0 ; OAN HAN
> 19 20 2 0.143 8180000.0 0.143 8180000.0 ; CAO OAP
> 20 21 2 0.100 15700000.0 0.100 15700000.0 ; OAP HAQ
> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 6 1 ; OAF CAC
> 2 7 1 ; PAE CAB
> 3 6 1 ; OAG CAC
> 4 6 1 ; OAH CAC
> 5 8 1 ; OAD OAA
> 5 10 1 ; OAD CAI
> 6 9 1 ; CAC HAA
> 6 11 1 ; CAC OAJ
> 6 13 1 ; CAC CAK
> 7 12 1 ; CAB HAJ
> 7 14 1 ; CAB OAL
> 7 16 1 ; CAB CAM
> 8 11 1 ; OAA OAJ
> 8 13 1 ; OAA CAK
> 9 10 1 ; HAA CAI
> 10 15 1 ; CAI HAL
> 10 17 1 ; CAI OAN
> 10 19 1 ; CAI CAO
> 11 14 1 ; OAJ OAL
> 11 16 1 ; OAJ CAM
> 12 13 1 ; HAJ CAK
> 13 18 1 ; CAK HAN
> 13 20 1 ; CAK OAP
> 14 17 1 ; OAL OAN
> 14 19 1 ; OAL CAO
> 15 16 1 ; HAL CAM
> 16 21 1 ; CAM HAQ
> 17 20 1 ; OAN OAP
> 18 19 1 ; HAN CAO
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 2 120.0 780.0 120.0 780.0 ; OAF PAE
> OAG
> 1 2 4 2 120.0 780.0 120.0 780.0 ; OAF PAE
> OAH
> 1 2 5 2 109.6 450.0 109.6 450.0 ; OAF PAE
> OAD
> 3 2 4 2 120.0 780.0 120.0 780.0 ; OAG PAE
> OAH
> 3 2 5 2 109.6 450.0 109.6 450.0 ; OAG PAE
> OAD
> 4 2 5 2 109.6 450.0 109.6 450.0 ; OAH PAE
> OAD
> 2 5 6 2 120.0 530.0 120.0 530.0 ; PAE OAD
> CAC
> 5 6 7 2 109.5 520.0 109.5 520.0 ; OAD CAC
> CAB
> 6 7 8 2 115.0 610.0 115.0 610.0 ; CAC CAB
> OAA
> 6 7 10 2 115.0 610.0 115.0 610.0 ; CAC CAB
> CAI
> 8 7 10 2 115.0 610.0 115.0 610.0 ; OAA CAB
> CAI
> 7 8 9 2 109.5 450.0 109.5 450.0 ; CAB OAA
> HAA
> 7 10 11 2 115.0 610.0 115.0 610.0 ; CAB CAI
> OAJ
> 7 10 13 2 115.0 610.0 115.0 610.0 ; CAB CAI
> CAK
> 11 10 13 2 115.0 610.0 115.0 610.0 ; OAJ CAI
> CAK
> 10 11 12 2 109.5 450.0 109.5 450.0 ; CAI OAJ
> HAJ
> 10 13 14 2 115.0 610.0 115.0 610.0 ; CAI CAK
> OAL
> 10 13 16 2 115.0 610.0 115.0 610.0 ; CAI CAK
> CAM
> 14 13 16 2 115.0 610.0 115.0 610.0 ; OAL CAK
> CAM
> 13 14 15 2 109.5 450.0 109.5 450.0 ; CAK OAL
> HAL
> 13 16 17 2 115.0 610.0 115.0 610.0 ; CAK CAM
> OAN
> 13 16 19 2 115.0 610.0 115.0 610.0 ; CAK CAM
> CAO
> 17 16 19 2 115.0 610.0 115.0 610.0 ; OAN CAM
> CAO
> 16 17 18 2 109.5 450.0 109.5 450.0 ; CAM OAN
> HAN
> 16 19 20 2 109.5 520.0 109.5 520.0 ; CAM CAO
> OAP
> 19 20 21 2 109.5 450.0 109.5 450.0 ; CAO OAP
> HAQ
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 2 1 3 4 2 35.3 334.8 35.3 334.8 ; imp PAE OAF
> OAG OAH
> 7 6 8 10 2 0.0 167.4 0.0 167.4 ; imp CAB CAC
> OAA CAI
> 10 13 11 7 2 0.0 167.4 0.0 167.4 ; imp CAI CAK
> OAJ CAB
> 13 16 14 10 2 0.0 167.4 0.0 167.4 ; imp CAK CAM
> OAL CAI
> 16 19 17 13 2 0.0 167.4 0.0 167.4 ; imp CAM CAO
> OAN CAK
> 6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; dih CAC OAD
> PAE OAF
> 7 6 5 2 1 0.0 1.3 3 0.0 1.3 3 ; dih CAB CAC
> OAD PAE
> 5 6 7 10 1 0.0 1.0 6 0.0 1.0 6 ; dih OAD CAC
> CAB CAI
> 6 7 8 9 1 180.0 16.7 2 180.0 16.7 2 ; dih CAC CAB
> OAA HAA
> 13 10 7 6 1 180.0 5.9 2 180.0 5.9 2 ; dih CAK CAI
> CAB CAC
> 7 10 11 12 1 180.0 16.7 2 180.0 16.7 2 ; dih CAB CAI
> OAJ HAJ
> 16 13 10 7 1 180.0 5.9 2 180.0 5.9 2 ; dih CAM CAK
> CAI CAB
> 10 13 14 15 1 180.0 16.7 2 180.0 16.7 2 ; dih CAI CAK
> OAL HAL
> 19 16 13 10 1 180.0 5.9 2 180.0 5.9 2 ; dih CAO CAM
> CAK CAI
> 13 16 17 18 1 180.0 16.7 2 180.0 16.7 2 ; dih CAK CAM
> OAN HAN
> 20 19 16 13 1 0.0 1.0 6 0.0 1.0 6 ; dih OAP CAO
> CAM CAK
> 16 19 20 21 1 0.0 1.3 3 0.0 1.3 3 ; dih CAM CAO
> OAP HAQ
>
>
> thanks a lot
>
--
==================================================
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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