[gmx-users] Incorrect bond in top file
Shima Arasteh
shima_arasteh2001 at yahoo.com
Mon Aug 27 20:35:01 CEST 2012
Please take a look at the .top file generated:
1 C 1 FVAL CN 1 0.357 12.011 ; qtot 0.357
2 HA 1 FVAL H1 2 0.1 1.008 ; qtot 0.457
3 O 1 FVAL ON 3 -0.51 15.999 ; qtot -0.053
4 NH1 1 FVAL N 4 -0.423 14.007 ; qtot -0.476
5 H 1 FVAL HN 5 0.333 1.008 ; qtot -0.143
6 CT1 1 FVAL CA 6 0.034 12.011 ; qtot -0.109
7 HB 1 FVAL HA 7 0.09 1.008 ; qtot -0.019
8 CT1 1 FVAL CB 8 -0.093 12.011 ; qtot -0.112
9 HA 1 FVAL HB 9 0.09 1.008 ; qtot -0.022
10 CT3 1 FVAL CG1 10 -0.268 12.011 ; qtot -0.29
11 HA 1 FVAL HG11 11 0.09 1.008 ; qtot -0.2
12 HA 1 FVAL HG12 12 0.09 1.008 ; qtot -0.11
13 HA 1 FVAL HG13 13 0.09 1.008 ; qtot -0.02
14 CT3 1 FVAL CG2 14 -0.268 12.011 ; qtot -0.288
15 HA 1 FVAL HG21 15 0.09 1.008 ; qtot -0.198
16 HA 1 FVAL HG22 16 0.09 1.008 ; qtot -0.108
17 HA 1 FVAL HG23 17 0.09 1.008 ; qtot -0.018
18 C 1 FVAL C 18 0.528 12.011 ; qtot 0.51
19 O 1 FVAL O 19 -0.51 15.999 ; qtot 0
; residue 2 SER rtp SER q 0.0
20 NH1 2 SER N 20 -0.47 14.007 ; qtot -0.47
I visualized the .gro file, found CN-HN bond.
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc:
Sent: Monday, August 27, 2012 10:45 PM
Subject: Re: [gmx-users] Incorrect bond in top file
On 8/27/12 1:31 PM, Shima Arasteh wrote:
> :D
> Hope so ( for your caps lock )! ;)
> Thanks, I'm happy!
>
> The relevant rtp file:
>
>
> [ FVAL ]
> [ atoms ]
> CN C 0.357 0
> ON O -0.51 1
> H1 HA 0.100 2
> N NH1 -0.423 3
> HN H 0.333 4
> CA CT1 0.034 5
> HA HB 0.09 6
> CB CT1 -0.093 7
> HB HA 0.09 8
> CG1 CT3 -0.268 9
> HG11 HA 0.09 10
> HG12 HA 0.09 11
> HG13 HA 0.09 12
> CG2 CT3 -0.268 13
> HG21 HA 0.09 14
> HG22 HA 0.09 15
> HG23 HA 0.09 16
> C C 0.528 17
> O O -0.510 18
> [ bonds ]
> CN H1
> CN ON
> CN N
> N HN
> CA N
> CA HA
> CA C
> C O
> CA CB
> CB HB
> CB CG1
> CB CG2
> CG2 HG21
> CG2 HG22
> CG2 HG23
> CG1 HG11
> CG1 HG12
> CG1 HG13
>
> [ impropers ]
> CN N ON H1
>
> The relevant .hdb file:
>
> FVAL 6
> 1 1 H1 CN N ON
> 1 1 HN N C CA
> 1 5 HA CA N C CB
> 1 5 HB CB CA CG1 CG2
> 3 4 HG1 CG1 CB CA
> 3 4 HG2 CG2 CB CA
>
I see nothing out of the ordinary here. You're saying that HN is bonded to CN
after running pdb2gmx?
-Justin
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Monday, August 27, 2012 8:39 PM
> Subject: Re: [gmx-users] Incorrect bond in top file
>
>
>
> On 8/27/12 11:41 AM, Shima Arasteh wrote:
>>
>>
>> Dear users,
>>
>>
>> [ Especially dear Justin ( please don't shout at me! ) ],
>>
>
> I haven't, and won't. I keep my caps lock off ;) Hopefully no one gets the
> impression that I have done otherwise...
>
>>
>> As I have described it many times, I defined a new residue named FVAL in aminoacids.rtp of the force field ( CHARMM36). The first step is "generating top file". When I ran the command of pdb2gmx, the top file is generated, but it contains a bond which I have not defined in the FVAL. The incorrect bond is between H-atom of valine ( this H is one of the atoms connected to the N of valine and this N is in the backbone, The N of valine is connected to C of formyl, CA and H) and C-atom of formyl group! ( It seems that the C of formyl doesn't form a second ordered bond with O ).
>>
>> aminoacids.hdb and aminoacids.rtp are the files I modified.
>>
>
> Please post the relevant .rtp and .hdb entries. There is an error somewhere,
> but we can't determine what it is without seeing these.
>
> -Justin
>
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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