Thanks dac. You got the problem right. I used tleap in Amber 9 to generate
the pdb file and used Amber 12 to run MD.
All in all, the answer I really want to know is, are the MD and free energy
calculation results reliable? Thanks.
------------------------------
Message: 11
Date: Fri, 25 Jul 2014 16:35:03 +0800
From: cq y <cuhkcuhk1234.gmail.com>
Subject: [AMBER] element symbol error in tleap
To: amber.ambermd.org
Message-ID:
<CAOOH8KYCZd4FPyJEb6b-1TQsnt7ApTBw4bZWeX6L_bFW43SuxQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear experts,
I suddenly found that a pdb file which I use ambpdb script to generate
looks like this.
ATOM 10377 CA NMG 684 52.546 49.086 64.805 0.00 0.00 C
ATOM 10378 1HA NMG 684 51.564 49.216 64.350 0.00 0.00 1
ATOM 10379 2HA NMG 684 52.607 48.601 65.779 0.00 0.00 2
ATOM 10380 C NMG 684 53.245 48.102 63.859 0.00 0.00 C
where NMG is the name of a non-standard residue. Note that the elements in
red color. Normally the numbers 1 and 2 should be element H. Does this
affect the MD as well as the MM_GBSA free energy results? The error
happened in the ligand structure.
Look forward to your reply.
Sincerely yours,
Jack
------------------------------
Message: 12
Date: Fri, 25 Jul 2014 16:52:40 +0800
From: Changqing Yan <ycqchemical.gmail.com>
Subject: [AMBER] element symbol error in tleap
To: amber.ambermd.org
Message-ID:
<CADP=_hSx_Mk0Bv0c-xxP2bCgOrfoXA535oMtcTQejDf_yn=2yw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear experts,
I suddenly found that a pdb file which I use ambpdb script to generate
looks like this.
ATOM 10377 CA NMG 684 52.546 49.086 64.805 0.00 0.00 *C*
ATOM 10378 1HA NMG 684 51.564 49.216 64.350 0.00 0.00 *1*
ATOM 10379 2HA NMG 684 52.607 48.601 65.779 0.00 0.00 *2*
ATOM 10380 C NMG 684 53.245 48.102 63.859 0.00 0.00 *C*
where NMG is the name of a non-standard residue. Note that the elements in
red color. Normally the numbers 1 and 2 should be element H. Does this
affect the MD as well as the MM_GBSA free energy results? The error
happened in the ligand structure.
I checked the original mol2 file for the non-standard residue. The element
symbol are right however, as shown below:
2 CA -0.128891 0.758463 -1.045314 C 1 NMG
-0.0933 ****
3 1HA -0.061778 0.090460 -1.890037 *H * 1 NMG
0.0767 ****
4 2HA -0.141346 1.779741 -1.397777 *H* 1 NMG
0.0767 ****
5 C -1.419790 0.528572 -0.264945 C 1 NMG
0.5948 ****
So now I am confused. I really look forward to your reply.
Sincerely yours,
C.Q.
------------------------------
Message: 13
Date: Fri, 25 Jul 2014 17:19:16 +0800
From: Changqing Yan <ycqchemical.gmail.com>
Subject: Re: [AMBER] element symbol error in tleap
To: amber.ambermd.org
Message-ID:
<CADP=_hREHCehiSh1GP24mF=ub6L4nhH3AX3=b-ufgns2t+Rnkg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
By the way, the MD ran normally and reported no errors.
On Fri, Jul 25, 2014 at 4:52 PM, Changqing Yan <ycqchemical.gmail.com>
wrote:
> Dear experts,
>
> I suddenly found that a pdb file which I use ambpdb script to generate
> looks like this.
>
> ATOM 10377 CA NMG 684 52.546 49.086 64.805 0.00 0.00 *C*
> ATOM 10378 1HA NMG 684 51.564 49.216 64.350 0.00 0.00 *1*
> ATOM 10379 2HA NMG 684 52.607 48.601 65.779 0.00 0.00 *2*
> ATOM 10380 C NMG 684 53.245 48.102 63.859 0.00 0.00
> *C*
>
> where NMG is the name of a non-standard residue. Note that the elements in
> red color. Normally the numbers 1 and 2 should be element H. Does this
> affect the MD as well as the MM_GBSA free energy results? The error
> happened in the ligand structure.
>
> I checked the original mol2 file for the non-standard residue. The element
> symbol are right however, as shown below:
>
> 2 CA -0.128891 0.758463 -1.045314 C 1 NMG
> -0.0933 ****
> 3 1HA -0.061778 0.090460 -1.890037 *H * 1 NMG
> 0.0767 ****
> 4 2HA -0.141346 1.779741 -1.397777 *H* 1 NMG
> 0.0767 ****
> 5 C -1.419790 0.528572 -0.264945 C 1 NMG
> 0.5948 ****
>
> So now I am confused. I really look forward to your reply.
>
> Sincerely yours,
> C.Q.
>
------------------------------
Message: 17
Date: Fri, 25 Jul 2014 07:23:54 -0400
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] element symbol error in tleap
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20140725112354.GB94100.biomaps.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Fri, Jul 25, 2014, Changqing Yan wrote:
>
> I suddenly found that a pdb file which I use ambpdb script to generate
> looks like this.
>
> ATOM 10377 CA NMG 684 52.546 49.086 64.805 0.00 0.00 *C*
> ATOM 10378 1HA NMG 684 51.564 49.216 64.350 0.00 0.00 *1*
> ATOM 10379 2HA NMG 684 52.607 48.601 65.779 0.00 0.00 *2*
> ATOM 10380 C NMG 684 53.245 48.102 63.859 0.00 0.00
*C*
This looks like output from an old version of AmberTools(?). The original
algorithm tried to determine the element from the atomic name. Now, atomic
numbers are stored in the prmtop file, and used to generate element names.
If at all possible, you should now be using AmberTools14.
If you have a non-standard residue, you can make up your own names, of
course,
but it is often helpful to use the names assigned by the PDB, if those are
available. Names like "1HA" look like holdovers from the very old PDB
(version 2) way of writing PDB files. You may want to consider using names
like HA1 and HA2 instead.
....dac
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Received on Fri Jul 25 2014 - 19:30:02 PDT
