At a fresh check this morning, the residue number 4 in the for-last
column of the mol2 file was the problem. Replacing 4 with 1, the mol2
file was loaded by xleap. Now I'll see if I can build prmtop/inpcrd
for the peptide.
francesco pietra
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Thu, Sep 30, 2010 at 6:35 PM
Subject: Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber
To: AMBER Mailing List <amber.ambermd.org>
On Thu, Sep 30, 2010 at 4:24 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Sep 30, 2010, Francesco Pietra wrote:
>
>>
>> My task is preparing prmtop/inpcrd for a peptide containing
>> phenylalanine amide. This is why I tried to get prepin/frcmod files to
>> feed to leap along with the pdb file of the peptide. Could you please
>> suggest a promising move from here?
>
> Use the mol2 file instead of prepi; we would like to retire prepi anyway,
> since it is an Amber-only format, whereas mol2 is widely used.
I must check the status of my tools, not used for Amber for a while.
Something must be out of order. In fact:
$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leapcrd.ff99SB
source leaprc.gaff
x = loadmol2 pha.mol2
It does not proceed. "top -i" shows a line for "xaleap" without any
advancement for at least 30 minutes. The xleap window is like dead.
A check with the sustiva tutorial showed sustiva.mol2 immediately
loaded on xleap (although the final prmtop/inpcrd are not accepted by
Chimera, while with VMD one of the phenyl CH is largely out of the
plane of the other five CHs).
I dare adding here pha.mol2 - generated with antechamber - which opens
correctly with VMD:
.<TRIPOS>MOLECULE
PHA
25 25 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 N -1.4440 -3.1720 1.4630 n4 4 PHA -0.824700
2 CA -1.4110 -3.3770 2.9090 c3 4 PHA 0.036000
3 CB -0.4300 -4.5020 3.2900 c3 4 PHA -0.048600
4 CG 0.9780 -4.2990 2.7780 ca 4 PHA -0.175300
5 CD1 1.3130 -4.6540 1.4600 ca 4 PHA -0.144600
6 CD2 1.9830 -3.7920 3.6150 ca 4 PHA -0.121900
7 CE1 2.5920 -4.3990 0.9590 ca 4 PHA -0.116400
8 CE2 3.2690 -3.5500 3.1200 ca 4 PHA -0.114500
9 CZ 3.5700 -3.8370 1.7840 ca 4 PHA -0.094400
10 C -1.1250 -2.0320 3.5690 c 4 PHA 0.644800
11 O -0.1320 -1.7830 4.2090 o 4 PHA -0.598600
12 N2 -2.0430 -1.0570 3.4130 n 4 PHA -0.624700
13 H -0.6440 -2.6240 1.1830 hn 4 PHA 0.480300
14 HA -2.4080 -3.6900 3.2200 hx 4 PHA 0.116800
15 HB2 -0.3920 -4.5680 4.3770 hc 4 PHA 0.097800
16 HB3 -0.8110 -5.4450 2.8970 hc 4 PHA 0.091500
17 HD1 0.5760 -5.1280 0.8290 ha 4 PHA 0.138400
18 HD2 1.7620 -3.5860 4.6520 ha 4 PHA 0.148300
19 HE1 2.8250 -4.6370 -0.0680 ha 4 PHA 0.158800
20 HE2 4.0290 -3.1420 3.7690 ha 4 PHA 0.161100
21 HZ 4.5540 -3.6250 1.3920 ha 4 PHA 0.162100
22 H21 -2.8820 -1.2340 2.8790 hn 4 PHA 0.332300
23 H22 -1.8920 -0.1500 3.8300 hn 4 PHA 0.358000
24 H1 -1.4190 -4.0670 0.9950 hn 4 PHA 0.472700
25 H2 -2.2920 -2.6840 1.2110 hn 4 PHA 0.464800
.<TRIPOS>BOND
1 1 2 1
2 1 13 1
3 1 24 1
4 1 25 1
5 2 3 1
6 2 10 1
7 2 14 1
8 3 4 1
9 3 15 1
10 3 16 1
11 4 5 ar
12 4 6 ar
13 5 7 ar
14 5 17 1
15 6 8 ar
16 6 18 1
17 7 9 ar
18 7 19 1
19 8 9 ar
20 8 20 1
21 9 21 1
22 10 11 2
23 10 12 1
24 12 22 1
25 12 23 1
.<TRIPOS>SUBSTRUCTURE
1 PHA 1 TEMP 0 **** **** 0 ROOT
>
>>> These prepin and frcmod file are not accepted by Chimera, while VMD
>>> shows a highly deformed structure (much too long C=O bond, phenyl
>>> hydrogens out of plane and ring distorted; NH3 also distorted.
>
> What options did you use in VMD? I don't see anything obvious that would
> allow VMD to read an Amber prepi file.
Sorry, I meant from prmtop/inpcrd created with leap.
Thanks for you kind help. francesco pietra
> What happens if you convert the prepi
> file back to mol2 or pdb format using antechamber?
Not tried yet due to the mess above.
>
>
> ....dac
>
>
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Received on Fri Oct 01 2010 - 03:30:03 PDT
